Benjamin N. Sacks

Population structure of California coyotes corresponds to habitat-specific breaks and illuminates species history

Little is known about the relationship between animal movements and the emergent structure of populations, especially for species occupying large continuous distributions. Some such mammals disperse disproportionately into habitat similar to their natal habitat, a behavioural bias that might be expected to lead to habitat‐conforming genetic structure. We hypothesized that coyotes (Canis latrans) would exhibit such natal‐biased dispersal, and used 13 microsatellite loci to test, correspondingly, whether genetic structure conformed to major habitat breaks. First, we used a model‐based approach to assign coyote genotypes to distinct genetic clusters irrespective of geographical location. Visualization on a geographical information system revealed a strong concordance between the locations of cluster assignments and habitat bioregions, not explainable in terms of physical dispersal barriers or intervening low‐quality habitat. Next, we used a multiple Mantel test, which controlled for effects of geographical distance (itself, marginally significant; P = 0.06), to statistically determine that genetic distance was indeed higher between than within bioregions (P < 0.001). Whereas previously published examples of landscape effects on gene flow have typically been explainable in terms of species‐wide habitat affinities or dispersal barriers, our finding that genetic subdivisions were associated with unobstructed boundaries between contiguous habitats suggests a role for intraspecific variability in habitat affinities as a factor underlying genetic structure. In addition, our data combined with previously published data suggest a pattern of genetic isolation‐by‐distance throughout western North America, consistent with independent evidence that the western half of the coyote range predates European settlement.

Phylogeography of the North American red fox: vicariance in Pleistocene forest refugia

Fossil, archaeological, and morphometric data suggest that indigenous red foxes in North America were derived from vicariance in two disjunct refugia during the last glaciation: one in Beringia and one in the contiguous USA. To test this hypothesis, we conducted a phylogeographical analysis of the North American red fox within its presettlement range. We sequenced portions of the mitochondrial cytochrome b (354 bp) gene and D‐loop (342 bp) from 220 historical red fox specimens. Phylogenetic analysis of the cytochrome b gene produced two clades that diverged c. 400 000 years before present (bp): a Holarctic and a Nearctic clade. D‐loop analyses of the Nearctic clade indicated three distinct subclades (≥ 99% Bayesian posterior probability); two that were more recently derived (rho estimate c. 20 000 bp) and were restricted to the southwestern mountains and the eastern portion of North America, and one that was older (rho estimate c. 45 000 bp) and more widespread in North America. Populations that migrated north from the southern refugium following deglaciation were derived from the colonization of North America during or prior to the Illinoian glaciation (300 000–130 000 bp), whereas populations that migrated south from the northern refugium represent a more recent colonization event during the Wisconsin glaciation (100 000–10 000 bp). Our findings indicate that Nearctic clade red foxes are phylogenetically distinct from their Holarctic counterparts, and reflect long‐term isolation in two disjunct forest refugia during the Pleistocene. The montane lineage, which includes endangered populations, may be ecologically and evolutionarily distinct.

Territoriality and breeding status of coyotes relative to sheep predation

Coyote (Cauis latrans) depredation is a chronic problem for sheep producers in the western United States. Due to increasingly localized control efforts, behavior of individual coyotes in sheep-ranching environments is becoming a more important consideration. We radiotracked 14 coyotes on a year-round sheep-ranching facility in north-coastal California during September 1993-December 1995. Breeding coyote pairs used mutually exclusive territories (maximum overlap between 90% adaptive kernel home ranges = 4%). Nonbreeding coyotes were transient or varied in their degree of fidelity to putative natal territories but generally avoided cores of nonnatal territories. Breeding coyotes whose territories contained sheep were the principal predators of sheep. In the 1994 lambing period (1 Jan-31 May). radiotelemetry indicated that 1 breeding male was responsible for 71% of 65 kills. In the 1995 lambing period, 4 breeding pairs were strongly implicated in 92% of 48 kills and were suspected of 85% of 26 additional kills; nonbreeders were not associated with sheep depredation. Depredation was reduced only when territorial breeders known to kill sheep were removed. These results suggest the need for management to target breeding adults in the immediate vicinity of depredation. Efforts to remove individuals > 1 territory-width away from problem sites are unlikely to reduce depredation and may exacerbate the problem by creating vacancies for new breeders that might kill sheep.

Relative Vulnerability of Coyotes to Removal Methods on a Northern California Ranch

Stable URL:http://links.jstor.org/sici?sici=0022-541X%28199907%2963%3A3%3C939%3ARVOCTR%3E2.0.CO%3B2-LThe Journal of Wildlife Management is currently published by Alliance Communications Group.Your use of the JSTOR archive indicates your acceptance of JSTORs Terms and Conditions of Use, available athttp://www.jstor.org/about/terms.html. JSTORs Terms and Conditions of Use provides, in part, that unless you have obtainedprior permission, you may not download an entire issue of a journal or multiple copies of articles, and you may use content inthe JSTOR archive only for your personal, non-commercial use.Please contact the publisher regarding any further use of this work. Publisher contact information may be obtained athttp://www.jstor.org/journals/acg.html.Each copy of any part of a JSTOR transmission must contain the same copyright notice that appears on the screen or printedpage of such transmission.The JSTOR Archive is a trusted digital repository providing for long-term preservation and access to leading academicjournals and scholarly literature from around the world. The Archive is supported by libraries, scholarly societies, publishers,and foundations. It is an initiative of JSTOR, a not-for-profit organization with a mission to help the scholarly community takeadvantage of advances in technology. For more information regarding JSTOR, please contact support@jstor.org.http://www.jstor.orgFri Oct 26 13:06:05 2007

Coyote movements and social structure along a cryptic population genetic subdivision

A recent region‐wide study determined that the central California coyote (Canis latrans) population was genetically subdivided according to habitat bioregions, supporting the hypothesis that coyotes exhibit a dispersal bias toward their natal habitat type. Here, we further investigated this hypothesis using radio‐collared coyotes captured on a 150‐km2 study site on the border of (i.e. overlapping) two bioregions (Great Valley and Cascade Mountains). As predicted, most coyotes were assigned (based on a priori genetic criteria) to genetic clusters corresponding to one of these two bioregions. All of those assigned to the Great Valley genetic cluster were caught in (and for the most part, remained in) the Great Valley bioregion. However, contrary to expectations, the coyotes assigned to the Cascades genetic cluster occurred commonly in both bioregions. Nearly all resident individuals on the study site, regardless of the particular bioregion, were assigned to the Cascades genetic cluster, whereas a sizable fraction of nonresident (transient or dispersing) coyotes caught in the Great Valley bioregion were assigned to the Great Valley cluster. Even among resident coyotes, interrelatedness of packs was greater within than between bioregions, and packs with territories overlapping both bioregions were more closely related to those with territories completely within the Cascades bioregion than territories completely within the Great Valley bioregion. Finally, direct estimates indicated that gene flow was twice as high from the Cascades bioregion to the Great Valley bioregion than in the reverse direction. Collectively, these findings reveal the anatomy of the genetic subdivision as beginning abruptly at the bioregion boundary and ending diffusely within the Great Valley bioregion.

The effectiveness of selective removal of breeding coyotes in reducing sheep predation

We evaluated the effect on sheep losses of selectively removing breeding coyotes (Canis latrans) from territories experiencing depredations. Breeding pairs of coyotes were the primary predators of sheep, and they killed sheep only within or on the periphery of their territories. Removal of either or both members of a breeding pair reduced or eliminated predation in that territory during the subsequent 3-month period. Killing of sheep by coyotes d sooner in territories that overlapped lambing pastures than in those that did not. For territories with access to lambs, the average time interval until killing of lambs resumed (43 days) approximated the time for a replacement pair of coyotes to become established. Removals of breeding coyotes during the nonlambing season did not reduce losses during the following lambing season. Although <33% as many coyotes were removed per unit time during selective control as during nonselective control, lambing-season lamb losses were lowest during the selective removal period. During the nonlambing period (when predation on sheep was low) sheep losses were similar under selective, nonselective, and no control. These results suggest that selective targeting of breeding coyotes, which is more socially acceptable than nonselective population reduction, also can be more effective in reducing sheep losses.

Y Chromosome Analysis of Dingoes and Southeast Asian Village Dogs Suggests a Neolithic Continental Expansion from Southeast Asia Followed by Multiple Austronesian Dispersals

Dogs originated more than 14,000 BP, but the location(s) where they first arose is uncertain. The earliest archeological evidence of ancient dogs was discovered in Europe and the Middle East, some 5-7 millennia before that from Southeast Asia. However, mitochondrial DNA analyses suggest that most modern dogs derive from Southeast Asia, which has fueled the controversial hypothesis that dog domestication originated in this region despite the lack of supporting archeological evidence. We propose and investigate with Y chromosomes an alternative hypothesis for the proximate origins of dogs from Southeast Asia--a massive Neolithic expansion of dogs from this region that largely replaced more primitive dogs to the west and north. Previous attempts to test matrilineal findings with independent patrilineal markers have lacked the necessary genealogical resolution and mutation rate estimates. Here, we used Y chromosome genotypes, composed of 29 single-nucleotide polymorphism (SNPs) and 5 single tandem repeats (STRs), from 338 Australian dingoes, New Guinea singing dogs, and village dogs from Island Southeast Asia, along with modern European breed dogs, to estimate the evolutionary mutation rates of Y chromosome STRs based on calibration to the independently known age of the dingo population. Dingoes exhibited a unique haplogroup characterized by a single distinguishing SNP mutation and 14 STR haplotypes. The age of the European haplogroup was estimated to be only 1.7 times older than that of the dingo population, suggesting an origin during the Neolithic rather than the Paleolithic (as predicted by the Southeast Asian origins hypothesis). We hypothesize that isolation of Neolithic dogs from wolves in Southeast Asia was a key step accelerating their phenotypic transformation, enhancing their value in trade and as cargo, and enabling them to rapidly expand and replace more primitive dogs to the West. Our findings also suggest that dingoes could have arrived in Australia directly from Taiwan, independently of later dispersals of dogs through Thailand to Island Southeast Asia.

Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins

Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (Canis lupus) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog.

A restricted hybrid zone between native and introduced red fox (Vulpes vulpes) populations suggests reproductive barriers and competitive exclusion.

Introduced species can threaten native taxa in multiple ways, including competition and hybridization, which can reduce fitness, alter ecological niches or swamp native genomes. Encroachment and hybridization by introduced species also provide opportunities to study the dynamics of invasiveness and hybridization during early stages following contact. We used 33 microsatellites, 51 single nucleotide polymorphisms and a mtDNA marker to characterize the extent and spatial pattern of encroachment and hybridization between a native, endemic subspecies of red fox (Vulpes vulpes patwin) and an introduced red fox population composed of highly admixed, phylogenetically divergent stock, resulting from a century of domestication. Both nuclear and mtDNA markers indicated that hybridization was primarily restricted to a narrow zone where the two populations came into contact. Although a few introgressed genotypes were detected in the interior of the native range, we found no immigrant foxes or F1 or F2 hybrids there, suggesting native foxes excluded introduced individuals. We speculate that the observed interbreeding at the periphery was facilitated by low densities. In total, 98% of mtDNA haplotypes in the native range were native and 96% of the nuclear ancestry was estimated to be native. Although the introduced range had expanded fivefold over the past four decades, native and non‐native haplotypes from museum samples collected in and near the native range three decades earlier showed a similar geographic distribution as today, suggesting that the native range and hybrid zone were relatively stable. We hypothesize that the monogamous mating system of red foxes and other wild canids may enhance their resistance to hybridization because of greater fitness consequences associated with mate discrimination.

Landscape characteristics influence morphological and genetic differentiation in a widespread raptor (Buteo jamaicensis).

Landscape‐scale population genetic structure in vagile vertebrates was commonly considered to be a contradiction in terms whereas recent studies have demonstrated behaviour and habitat associated structure in several such species. We investigate whether landscape features influence morphological and genetic differentiation in a widespread, mobile raptor. To accurately describe genetic differentiation associated with regional landscape factors, we first investigated subspecies relationships at a continental scale. We used 17 microsatellite loci and five morphological measurements to investigate differentiation between eastern and western subspecies of red‐tailed hawks (Buteo jamaicensis) and to identify patterns between differentiation and habitat within western North America. Bayesian and frequency‐based analyses of microsatellite data revealed clear distinctions between B. j. borealis (eastern) and B. j. calurus (western) samples. Furthermore, hawks sampled in Texas were stouter than those collected from the Rocky Mountains and farther west. Among western samples, birds from the Great Basin, Rocky Mountains, and Washington were significantly different in morphology than those from Oregon and California. We identified a pattern of isolation by distance among western breeding sites around the Sierra Nevada. Given the long‐range dispersal capabilities of raptors, this pattern suggests that population‐specific habitat preferences, corresponding with habitat breaks between eastern and western slopes of the Sierra Nevada, and/or regionally variable population densities limit migration between the Mediterranean habitat of central California and the xeric habitats of southern California and interior west. We suggest habitat preferences and regionally disparate population densities may play a role in shaping genetic structure in vagile avian taxa.