Subspecific relationships and genetic structure in the spotted owl

Hierarchical genetic structure was examined in the three geographically-defined subspecies of spotted owl (Strix occidentalis) to define relationships among subspecies and quantify variation within and among regional and local populations. Sequences (522 bp) from domains I and II of the mitochondrial control region were analyzed for 213 individuals from 30 local breeding areas. Results confirmed significant differences between northern spotted owls and the other traditional geographically defined subspecies but did not provide support for subspecific level differences between California and Mexican spotted owls. Divergence times among subspecies estimated with a 936 bp portion of the cytochrome b gene dated Northern and California/Mexican spotted owl divergence time to 115,000–125,000 years ago, whereas California/Mexican spotted owl divergence was estimated at 15,000 years ago. Nested clade analyses indicated an association between California spotted owl and Mexican spotted owl haplotypes, implying historical contact between the two groups. Results also identified a number of individuals geographically classified as northern spotted owls (S. o. caurina) that contained haplotypes identified as California spotted owls (S. o. caurina). Among all northern spotted owls sampled (n=131), 12.9% contained California spotted owl haplotypes. In the Klamath region, which is the contact zone between the two subspecies, 20.3% (n=59) of owls were classified as California spotted owls. The Klamath region is a zone of hybridization and speciation for many other taxa as well. Analyses of population structure indicated gene flow among regions within geographically defined subspecies although there was significant differentiation among northern and southern regions of Mexican spotted owls. Among all areas examined, genetic diversity was not significantly reduced except in California spotted owls where the southern region consists of one haplotype. Our results indicate a stable contact zone between northern and California spotted owls, maintaining distinct subspecific haplotypes within their traditional ranges. This supports recovery efforts based on the traditional subspecies designation for the northern spotted owl. Further, although little variation was found between California and Mexican spotted owls, we suggest they should be managed separately because of current isolation between groups.     

Mito‐nuclear discordance across a recent contact zone for California voles

To examine the processes that maintain genetic diversity among closely related taxa, we investigated the dynamics of introgression across a contact zone between two lineages of California voles (Microtus californicus). We tested the prediction that introgression of nuclear loci would be greater than that for mitochondrial loci, assuming ongoing gene flow across the contact zone. We also predicted that genomic markers would show a mosaic pattern of differentiation across this zone, consistent with genomes that are semi‐permeable. Using mitochondrial cytochrome b sequences and genome‐wide loci developed via ddRAD‐seq, we analyzed genetic variation for 10 vole populations distributed along the central California coast; this transect included populations from within the distributions of both parental lineages as well as the putative contact zone. Our analyses revealed that (1) the two lineages examined are relatively young, having diverged ca. 8.5–54 kya, (2) voles from the contact zone in Santa Barbara County did not include F1 or early generation backcrossed individuals, and (3) there appeared to be little to no recurrent gene flow across the contact zone. Introgression patterns for mitochondrial and nuclear markers were not concordant; only mitochondrial markers revealed evidence of introgression, putatively due to historical hybridization. These differences in genetic signatures are intriguing given that the contact zone occurs in a region of continuous vole habitat, with no evidence of past or present physical barriers. Future studies that examine specific isolating mechanisms, such as microhabitat use and mate choice, will facilitate our understanding of how genetic boundaries are maintained in this system.     

Reproductive isolation between oviparous and viviparous lineages of the Eurasian common lizard Zootoca vivipara in a contact zone

Contact zones between two evolutionary lineages are often useful for understanding the process of speciation because the observed genetic pattern reflects the history of differentiation. The Eurasian lacertid lizard Zootoca vivipara is a potentially interesting model for studying the role of reproductive mode in the speciation of squamate reptiles because it has both oviparous (Zootoca vivipara carniolica) and viviparous (Zootoca vivipara vivipara) populations that have recently been shown to be genetically distinct. We studied a newly‐discovered syntopic area of these two Zootoca subspecies in the central Italian Alps using genetic markers to investigate the level of introgression between them. Patterns of genetic differentiation in a fragment of the mitochondrial DNA cytb gene and a set of nuclear microsatellites show that the speciation process is complete in this area, with no evidence of recent introgression. Phylogenetic and genotypic divergence suggests that the two subspecies have experienced long independent evolutionary histories, during which genetic and phenotypic differences evolved. The possible roles of biogeography, reproductive mode, and cytogenetic differentiation in this speciation process are discussed. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 566–573.     

The genetic isolation between some populations of Proasellus coxalis

We tested the reroductive compatibility existing between four geographically different populations of Proaselis coxalis (Crustacea Isopoda) collected in the river Sarno (near Naples) and on three Sicilian sites: San Domenico; Villa Grazia di Carini and Enna. By means of laboratory hybridization experiments (“no-choice” method) we investigated and characterized the reproductive isolation established between these populations under allopatric conditions. The populations San Domenico and Enna are reproductively isolated from Villa Grazia di Carini and Sarno, so that they may be considered as belonging to different species. The mechanism of reproductive isolation are of postzygotic nature only: embronic death, hbrid inviability and sterility of the surviving hybrids. These results agree with tie theory of aioatric speciation, according to which in the first phase of speciation only post-zygotic mechanisms occur as an accidental product of genetic divergence.     

Genetic differences and phenotypic plasticity in body size between high- and low-altitude populations of the ground beetle Carabus tosanus

The body size of a univoltine carabid beetle Carabus tosanus on Shikoku Island, Japan, was clearly smaller in higher‐altitude populations (subspecies), which possibly represents incipient speciation. To explore the determinants of altitudinal differences in body size in this species, we studied the degree of phenotypic plasticity by conducting rearing experiments at two constant temperatures and examined genetic differences through interpopulation crosses. At 15 °C, C. tosanus had a longer developmental period and a shorter adult body than at 20 °C. Nevertheless, variation in body size due to temperature effects (phenotypic plasticity) was small compared to the interpopulation differences, which suggests substantial genetic differences between populations (subspecies) at different altitudes. In F₁ offspring from crosses between a low‐altitude (subspecies tosanus) and a high‐altitude population (subspecies ishizuchianus), adult body length was affected by the genotypes of both parents, with an interaction effect of parental genotype and offspring sex. Further analyses revealed that adult body length was affected by sex‐linked factors in addition to autosomal factors. These genetic differences in body size may have resulted from adaptations to different altitudes and may be important for the process of incipient speciation because body size differences could contribute to premating reproductive isolation.     

Gut microbial diversity across a contact zone for California voles: Implications for lineage divergence of hosts and mitonuclear mismatch in the assembly of the mammalian gut microbiome

Gut microbial diversity is thought to reflect the co‐evolution of microbes and their hosts as well as current host‐specific attributes such as genetic background and environmental setting. To explore interactions among these parameters, we characterized variation in gut microbiome composition of California voles (Microtus californicus) across a contact zone between two recently diverged lineages of this species. Because this contact zone contains individuals with mismatched mitochondrial‐nuclear genomes (cybrids), it provides an important opportunity to explore how different components of the genotype contribute to gut microbial diversity. Analyses of bacterial 16S rRNA sequences and joint species distribution modelling revealed that host genotypes and genetic differentiation among host populations together explained more than 50% of microbial community variation across our sampling transect. The ranked importance (most to least) of factors contributing to gut microbial diversity in our study populations were: genome‐wide population differentiation, local environmental conditions, and host genotypes. However, differences in microbial communities among vole populations (β‐diversity) did not follow patterns of lineage divergence (i.e., phylosymbiosis). Instead, among‐population variation was best explained by the spatial distribution of hosts, as expected if the environment is a primary source of gut microbial diversity (i.e., dispersal limitation hypothesis). Across the contact zone, several bacterial taxa differed in relative abundance between the two parental lineages as well as among individuals with mismatched mitochondrial and nuclear genomes. Thus, genetic divergence among host lineages and mitonuclear genomic mismatches may also contribute to microbial diversity by altering interactions between host genomes and gut microbiota (i.e., hologenome speciation hypothesis).     

The maintenance of phenotypic divergence through sexual selection: An experimental study in barn swallows Hirundo rustica

Previous studies have shown that sexual signals can rapidly diverge among closely related species. However, we lack experimental studies to demonstrate that differences in trait‐associated reproductive performance maintain sexual trait differences between closely related populations, in support for a role of sexual selection in speciation. Populations of Northern Hemisphere distributed barn swallows Hirundo rustica are closely related, yet differ in two plumage‐based traits: ventral color and length of the outermost tail feathers (streamers). Here we provide experimental evidence that manipulations of these traits result in different reproductive consequences in two subspecies of barn swallow: (H. r. erythrogaster in North America and H. r. transitiva in the East Mediterranean). Experimental results in Colorado, USA, demonstrate that males with (1) darkened ventral coloration and (2) shortened streamers gained paternity between two successive reproductive bouts. In contrast, exaggeration of both traits improved reproductive performance within H. r. transitiva in Israel: males with a combination treatment of darkened ventral coloration and elongated streamers gained paternity between two successive reproductive bouts. Collectively, these experimental results fill an important gap in our understanding for how divergent sexual selection maintains phenotype differentiation in closely related populations, an important aspect of the speciation process.     

Speciation in Progress? A Continuum of Reproductive Isolation in <Emphasis Type="Italic">Drosophila Bipectinata</Emphasis>

Incipient species in the early stages of divergence can provide crucial information about the genetic basis of reproductive isolation and the evolutionary forces that promote speciation. In this report, we describe two subspecies of Drosophila bipectinata that show a continuum of reproductive isolation. Crosses between strains of the same subspecies produce fully fertile offspring. At the same time, each subspecies harbors extensive variation for the degree of reproductive isolation from the other subspecies. The percentage of fertile hybrid males varies from 0 to 90%, depending on the origin of parental strains, indicating that the genes responsible for hybrid sterility are not fixed within either subspecies, or even within local populations. Reproductive isolation is non-transitive, so that the extent of hybrid sterility depends on the particular combination of strains. The two subspecies show little or no evidence of genetic differentiation at three nuclear loci, suggesting that they diverged very recently or continue to experience significant levels of gene flow. A hybrid zone between the two subspecies may exist in New Guinea and Northeastern Australia.     

Population genetic isolation and limited connectivity in the purple finch (Haemorhous purpureus)

Using a combination of mitochondrial and z‐linked sequences, microsatellite data, and spatio‐geographic modeling, we examined historical and contemporary factors influencing the population genetic structure of the purple finch (Haemorhous purpureus). Mitochondrial DNA data show the presence of two distinct groups corresponding to the two subspecies, H. p. purpureus and H. p. californicus. The two subspecies likely survived in separate refugia during the last glacial maximum, one on the Pacific Coast and one east of the Rocky Mountains, and now remain distinct lineages with little evidence of gene flow between them. Southwestern British Columbia is a notable exception, as subspecies mixing between central British Columbia and Vancouver Island populations suggests a possible contact zone in this region. Z‐linked data support two mitochondrial groups; however, Coastal Oregon and central British Columbia sites show evidence of mixing. Contemporary population structure based on microsatellite data identified at least six genetic clusters: three H. p. purpureus clusters, two H. p. californicus clusters, and one mixed cluster, which likely resulted from high site fidelity and isolation by distance, combined with sexual selection on morphological characters reinforcing subspecies differences.     

Use of Museum Specimens to Refine Historical Pronghorn Subspecies Boundaries

Endangered Sonoran (Antilocapra americana sonoriensis) and Peninsular (A. a. peninsularis) pronghorn persist largely because of captive breeding and reintroduction efforts. Recovery team managers want to re-establish pronghorn in their native range, but there is currently uncertainty regarding the subspecies status of extinct pronghorn populations that historically inhabited southern California, USA, and northern Baja California, Mexico. To address this uncertainty, we genotyped museum specimens and conducted phylogenetic and population genetic analyses of historical data in the context of 3 contemporary pronghorn populations. The historical northern Baja California pronghorn share the most ancestry with contemporary Peninsular pronghorn, whereas pronghorn in southern California share more ancestry with contemporary American (A. a. americana) pronghorn. For reintroductions into northern Baja California, the Peninsular subspecies is more appropriate based on museum genetic data. For reintroductions into Southern California, ecological and genetic factors are both important, as the subspecies most genetically related to historical populations (American) may not be well-adapted to the hot, low-elevation deserts of the reintroduction area. © 2019 The Wildlife Society.     

Genetic structure of California's elk: a legacy of extirpations,reintroductions, population expansions,and admixture

California, USA, is home to 3 subspecies of North American elk (Cervus canadensis): Roosevelt (C. c. roosevelti), Rocky Mountain (C. c. nelsoni), and tule (C. c. nannodes). Effective management requires a baseline understanding of each subspecies' range, admixture zones, and geographic patterns of genetic diversity. To address these questions, we genotyped 1,271 individual elk from California (n = 1,204) and reference populations of Rocky Mountain and Roosevelt elk from Nevada (n = 32) and Oregon (n = 35), USA. Using 19 polymorphic microsatellite loci, we detected admixture between Roosevelt and Rocky Mountain elk at a contact zone in northern California, and between Roosevelt and tule elk in north-coastal California and central-coastal California. We identified a genetically distinct population of Roosevelt elk in northwestern California, likely reflecting the remnant population that survived a large demographic decline from overhunting during the 1800s. Tule elk exhibited lower levels of heterozygosity (0.44 ± 0.03 [SD]) and allelic richness (2.9 ± 0.2) than Rocky Mountain (0.58 ± 0.05, 4.9 ± 0.4, respectively) and Roosevelt (0.50 ± 0.06, 4.4 ± 0.6, respectively) elk. Among tule elk populations, heterozygosity varied, with the lowest heterozygosity (0.23 ± 0.05) corresponding to the oldest enclosed herd used over the past century as a source of translocations. Among tule elk populations, genetic structure revealed several cases of successful and unsuccessful reintroduction or augmentation attempts. Results provide an essential baseline for future monitoring and decisions about harvest management, translocations to preserve genetic diversity, and landscape-level conservation planning to maintain, enhance, or obstruct connectivity of elk populations. Genome-wide sequencing and analyses are needed to quantify inbreeding absolutely and assess genetic load and the age of admixture where subspecies currently exchange genes.     

Investigations of fine-scale phylogeography in Tigriopus californicus reveal historical patterns of population divergence

Background  

The intertidal copepod Tigriopus californicus is a model for studying the process of genetic divergence in allopatry and for probing the nature of genetic changes that lead to reproductive isolation. Although previous studies have revealed a pattern of remarkably high levels of genetic divergence between the populations of this species at several spatial scales, it is not clear what types of historical processes are responsible. Particularly lacking are data that can yield insights into population history from the finest scales of geographic resolution.     

Rainfall, ambient temperature, and Clethrionomys californicus capture frequency

Sixty Western Red-backed Voles Clethrionomys californicus inhabiting an old-growth mixed conifer forest in north-western California (USA) were studied over 2 years to assess relationships among vole capture frequency, rainfall, and ambient temperature. Red-backed Voles were encountered more often and recapture rates per vole doubled with the tripling of yearly rainfall. In addition, more voles were captured during wet months than dry months. Analysed over weekly intervals, captures were positively correlated with the amount of weekly rainfall, a greater proportion of the known vole population was encountered during wet weeks than dry weeks, and increased weekly rainfall resulted in an increased proportion of the vole population captured. Significant relationships were not found between daily rainfall and vole captures, but both minimum and maximum daily ambient temperatures were lower when voles were trapped. Vole captures increased with decreases in daily and weekly minimum and maximum ambient temperatures. Weekly rainfall in combination with minimum weekly temperatures accounted for the greatest explanation of variability in vole capture frequencies. These results document that rainfall and ambient temperature have an impact on Western Red-backed Vole capture frequency; thus these weather variables should be addressed as covariates in analyses focused on capture data for this species.     

Speciation in the stonechat (Saxicola torquata) inferred from nucleotide sequences of the cytochrome-b gene

The geographical differentiation and speciation in the stonechat (Saxicola torquata; Aves: Turdidae) was studied by sequencing a 300-bp fragment of the mitochondrial cytochrome-b gene. Stonechats from three different subspecies inhabiting three continents (S. t. rubicola, the European stonechat; S. t. maura, the Siberian stonechat; and S. t. axillaris, an African stonechat) and stonechats from seven European populations were examined. While variation within the populations of the European subspecies was less than 0.3%, the genetic distances between the subspecies were substantial (2.7-5.7%) in comparison with published data for subspecies of other birds. If speciation is indeed reflected in the cytochrome-b gene of stonechats, species status for the African stonechat, but also for the Siberian taxon, should be reconsidered, especially in the light of differences in distributions, morphology and habitat preference.     

MORE THAN BINDIN DIVERGENCE: REPRODUCTIVE ISOLATION BETWEEN SYMPATRIC SUBSPECIES OF A SEA URCHIN BY ASYNCHRONOUS SPAWNING

The evolution of reproductive barriers is crucial to the process of speciation. In the Echinoidea, studies have focused on divergence in the gamete recognition protein, bindin, as the primary isolating mechanism among species. As such, the capacity of alternate mechanisms to be effective reproductive barriers and the phylogenetic context in which they arise is unclear. Here, we examine the evolutionary histories and factors limiting gene exchange between two subspecies of Heliocidaris erythrogramma that occur sympatrically in Western Australia. We found low, but significant differentiation between the subspecies in two mitochondrial genes. Further, coalescent analyses suggest that they diverged in isolation on the east and west coasts of Australia, with a subsequent range expansion of H. e. erythrogramma into Western Australia. Differentiation in bindin was minimal, indicating gamete incompatibility is an unlikely reproductive barrier. We did, however, detect strong asynchrony in spawning seasons; H. e. erythrogramma spawned over summer whereas H. e. armigera spawned in autumn. Taken together, we provide compelling evidence for a recent divergence of these subspecies and their reproductive isolation without gamete incompatibility. Western Australian H. erythrogramma may therefore present an intriguing case of incipient speciation, which depends on long‐term persistence of the factors underlying this spawning asynchrony.     

ADAPTATION TO DESICCATION FAILS TO GENERATE PRE‐ AND POSTMATING ISOLATION IN REPLICATE DROSOPHILA MELANOGASTER LABORATORY POPULATIONS

Many laboratory speciation experiments have raised allopatric populations in different environments to determine whether reproductive isolation evolves as a byproduct of adaptation (a form of ecological speciation). Few, however, have addressed the evolution of both pre‐ and postmating isolation or investigated the conditions affecting the process. We present results of an evolution experiment in which 12 lines of Drosophila melanogaster were derived from a common population and then independently evolved for more than 57 generations under alternative selection treatments. Six “desiccation” populations had access to food and water removed during a period of their adult lives generating strong desiccation selection, and six “starvation” populations had access to food but not water removed for the same period, generating a mild starvation stress. Substantial divergence of cuticular hydrocarbons occurred between the desiccation and starvation populations, key traits that have been implicated in sexual isolation in Drosophila. Despite this divergence, there was no detectable premating isolation between desiccation and starvation populations and postmating isolation was asymmetrical: the fitness of F1 hybrids was reduced in the desiccation but not the starvation environment. This asymmetry was likely caused by the absence of divergent selection: adaptation to desiccation appears to have come at no cost to performance in the starvation environment. Novel environments are thought to promote the evolution of reproductive isolation. Understanding the conditions that favor or hamper this remains a key challenge for speciation research.     

Genetics of mitochondrial glutamate-oxaloacetate transaminase (GOT-2) in Tigriopus californicus

Glutamate-oxaloacetate transaminase (GOT; EC 2.6.1.1) occurs as two electrophoretically distinguishable isozymes in the copepod Tigriopus californicus. The slower-migrating form, referred to as GOT2, is shown to be associated with the mitochondrial cell fraction. GOT2 phenotypes are inherited in typical Mendelian fashion, indicating that they are encoded by a nuclear gene. Allelic frequencies for electrophoretic variants of the two Got loci in 12 California populations of T. californicus show a sharp differentiation of local populations. Linkage studies demonstrated that Got-2 is linked to Got-1; a map of four loci in linkage group I is presented.This work was supported by NSF grant DEB-8207000 to R.S.B. and an NIH traineeship in Genetics to M.M.D.