Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae)

Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of North American freshwater fishes. With a near-complete taxon sampling of close to 250 species, we aim to investigate strategies for efficient multilocus data sampling and the estimation of divergence times using relaxed-clock methods when a clade lacks a fossil record. Our phylogenetic data set comprises a single mitochondrial DNA (mtDNA) gene and two nuclear genes sampled from 245 of the 248 darter species. This dense sampling allows us to determine if a modest amount of nuclear DNA sequence data can resolve relationships among closely related animal species. Darters lack a fossil record to provide age calibration priors in relaxed-clock analyses. Therefore, we use a near-complete species-sampled phylogeny of the perciform clade Centrarchidae, which has a rich fossil record, to assess two distinct strategies of external calibration in relaxed-clock divergence time estimates of darters: using ages inferred from the fossil record and molecular evolutionary rate estimates. Comparison of Bayesian phylogenies inferred from mtDNA and nuclear genes reveals that heterospecific mtDNA is present in approximately 12.5% of all darter species. We identify three patterns of mtDNA introgression in darters: proximal mtDNA transfer, which involves the transfer of mtDNA among extant and sympatric darter species, indeterminate introgression, which involves the transfer of mtDNA from a lineage that cannot be confidently identified because the introgressed haplotypes are not clearly referable to mtDNA haplotypes in any recognized species, and deep introgression, which is characterized by species diversification within a recipient clade subsequent to the transfer of heterospecific mtDNA. The results of our analyses indicate that DNA sequences sampled from single-copy nuclear genes can provide appreciable phylogenetic resolution for closely related animal species. A well-resolved near-complete species-sampled phylogeny of darters was estimated with Bayesian methods using a concatenated mtDNA and nuclear gene data set with all identified heterospecific mtDNA haplotypes treated as missing data. The relaxed-clock analyses resulted in very similar posterior age estimates across the three sampled genes and methods of calibration and therefore offer a viable strategy for estimating divergence times for clades that lack a fossil record. In addition, an informative rank-free clade-based classification of darters that preserves the rich history of nomenclature in the group and provides formal taxonomic communication of darter clades was constructed using the mtDNA and nuclear gene phylogeny. On the whole, the appeal of mtDNA for phylogeny inference among closely related animal species is diminished by the observations of extensive mtDNA introgression and by finding appreciable phylogenetic signal in a modest sampling of nuclear genes in our phylogenetic analyses of darters.     

USING CARBON AND NITROGEN ISOTOPE VALUES TO INVESTIGATE MATERNAL STRATEGIES IN NORTHEAST PACIFIC OTARIIDS

We examine the utility of stable carbon and nitrogen isotope variations to characterize the length of the nursing/lactation period and age at weaning for two northern Pacific otariid species, the northern fur seal (Callorhinus ursinus) and California sea lion (Zalophus californianus). We used two sampling strategies to measure ontogenetic trends in isotope value, and compared our results to observational data on the reproductive strategies used by these otariids. For Zalophus, we found evidence for ¹⁵N enrichment and ¹³C‐depletion in bone collagen representing the first and second year of growth, which is consistent with the ～12–14‐mo weaning age in this population after a suitable turnover rate for bone collagen is considered. Analysis of individual tooth annuli from a different suite of Zalophus specimens suggests that half of the individuals were weaned at ～12 mo of age, and half were dependent on milk for a portion of their second year. For Callorhinus, bone collagen for age classes that contain pre‐weaned individuals were ¹⁵N‐enriched, but values were significantly lower in specimens between 6 and 20 mo of age. These ¹⁵N‐enriched values, presumably acquired during nursing between 0 and 4 mo of age in Callorhinus, were not present in specimens older than 12 mo of age. Thus complete bone collagen turnover in young‐of‐the‐year occurs in 8–10 mo. ¹⁵N enrichment is evident in the first annulus of female Callorhinus individuals, but is not detectable in males. Analyses of Callorhinus tooth annuli show no ontogenetic trends in δ¹³C values. Our study indicates that nitrogen, and in some cases carbon, isotopes can be used to assess reproductive strategies in marine mammals. When coupled with accurate age estimates based on bone growth regressions, this isotopic technique can be applied to historical or fossil otariids to gain insight into the flexibility of maternal strategies within and across species.     

Genetic diversity and population parameters of sea otters, Enhydra lutris, before fur trade extirpation from 1741-1911

All existing sea otter, Enhydra lutris, populations have suffered at least one historic population bottleneck stemming from the fur trade extirpations of the eighteenth and nineteenth centuries. We examined genetic variation, gene flow, and population structure at five microsatellite loci in samples from five pre-fur trade populations throughout the sea otter's historical range: California, Oregon, Washington, Alaska, and Russia. We then compared those values to genetic diversity and population structure found within five modern sea otter populations throughout their current range: California, Prince William Sound, Amchitka Island, Southeast Alaska and Washington. We found twice the genetic diversity in the pre-fur trade populations when compared to modern sea otters, a level of diversity that was similar to levels that are found in other mammal populations that have not experienced population bottlenecks. Even with the significant loss in genetic diversity modern sea otters have retained historical structure. There was greater gene flow before extirpation than that found among modern sea otter populations but the difference was not statistically significant. The most dramatic effect of pre fur trade population extirpation was the loss of genetic diversity. For long term conservation of these populations increasing gene flow and the maintenance of remnant genetic diversity should be encouraged.     

GENETIC ANALYSIS OF KILLER WHALE (ORCINUS ORCA) HISTORICAL BONE AND TOOTH SAMPLES TO IDENTIFY WESTERN U.S. ECOTYPES

Little is known about the historical range of killer whale ecotypes in the eastern North Pacific (ENP). It is possible that ranges have shifted in the last few decades because of changes in availability of food. In particular, the southern resident ecotype, currently found primarily in the inland waters of Washington State, is known to prey extensively on salmon, which have declined in recent decades along the outer coasts of Washington, Oregon, and California. To investigate historical distributions of this and the other ENP ecotypes, samples of teeth and bones were obtained from NMFS and museum collections. We amplified a short section of the mitochondrial DNA control region that contains four diagnostic sites that differentiate between haplotypes found in ecotypes of ENP killer whales. Results did not show any southern resident haplotypes in samples from south of the Washington State inland waterways. One whale genetically identified as a northern resident extends the known southernmost distribution of the population from Oregon to California. Items of diet identified from stomach contents of six of the whales genetically identified to ecotype conformed with what is known of the feeding habits of the various ecotypes.     

Flexural and torsional stiffness in multi-jointed biological beams

Flexibility, the ability to deform in response to loads, is a common property of biological beams. This paper investigates the mechanical behavior of multi-jointed beams, which are characterized by a linear series of morphologically similar joints. Flexural stiffness and torsional stiffness were measured in two structurally distinct beams, crinoid arms (Echinodermata, Comatulida) and crustacean antennae (Arthropoda, Decapoda). Morphological data from these beams were used to determine the relative contributions of beam diameter and joint density (number of joints per millimeter of beam length) to the flexural and torsional stiffness of these two structures. As predicted by beam theory, beam diameter influenced stiffness in both crinoid arms and crustacean antennae. In crinoid arms, increases in joint density were associated with decreases in stiffness, but joint density had no significant influence on stiffness in crustacean antennae. In both crinoid arms and crustacean antennae, the magnitudes of flexural and torsional stiffness, as well as the ratio of these two variables, were similar to previously reported values for non-jointed biological beams. These results suggest that the structural design of a biological beam is not a limiting factor determining its mechanical properties.     

Twisting and bending of biological beams: distribution of biological beams in a stiffness mechanospace

Most biological beams bend and twist relatively easily compared to human-made structures. This paper investigates flexibility in 57 diverse biological beams in an effort to identify common patterns in the relationship between flexural stiffness and torsional stiffness. The patterns are investigated by mapping both ideal and biological beams into a mechanospace defined by flexural and torsional stiffness. The distribution of biological beams is not random, but is generally limited to particular regions of the mechanospace. Biological beams that are stiff in bending are stiff in torsion, while those that bend easily also twist easily. Unoccupied regions of the mechanospace represent rare combinations of mechanical properties, without proving that they are impossible. The mechanical properties of biological beams closely resemble theoretical expectations for ideal beams. Both distributions are potentially being driven by the interdependence of the material and structural properties determining stiffness. The mechanospace can be used as a broadly comparative tool to highlight systems that fall outside the general pattern observed in this study. These outlying beams may be of particular interest to both biologists and engineers due to either material or structural innovations.     

Defining and identifying sustainable harvests of resources: Archaeological examples of pinniped harvests in the eastern North Pacific

Archaeologists and resource managers are starting to recognize the value of studying ancient cultures for examples of how resources have, and have not, been sustainably utilized in the past as a way of understanding current trends in environmental degradation. These studies do not provide sweeping generalizations about aboriginal resource use but, rather, identify the range of conditions under which sustainable harvests may be possible. The hypothesis of sustainable harvests must be tested using variables that can be measured equally well in ancient (e.g., archaeological) and modern contexts.These factors are carefully considered in this analysis of pinniped (seal and sea lion) remains from two archaeological sites on the eastern North Pacific (ENP) coast, where pinnipeds have been hunted for millennia. Reconstruction of the age composition, or harvest profile, of Callorhinus ursinus at the Ozette Village Site, Washington, shows that males and females of all ages were harvested, and supports the hypothesis that it was done so sustainably for over 500 years. After this period of apparent stability, C. ursinus abandoned local breeding colonies in the early historic period. In contrast, harvests of this species at the Moss Landing Hill Site, California, primarily targeted young of the year, and sub-adult and adult females. While this harvest is also inferred to have targeted a local breeding colony, C. ursinus appear to have been extirpated nearly 2000 years earlier at Moss Landing than at Ozette.The causes of these extirpations are not known, but the timing does not correspond well with known climatic changes, suggesting that subsistence, and perhaps commercial, hunting may have played a role. These examples underscore the need to recognize that patterns of resource use are highly variable – different cultures have had varying levels of effects on economically important species, and these effects have varied temporally, spatially, and taxonomically.     

Postural role of lateral axial muscles in developing bottlenose dolphins (Tursiops truncatus)

Foetal dolphins (Tursiops truncatus) are bent ventrolaterally, such that the tailflukes and lower jaw are juxtaposed. The lateral flexibility required en utero may compromise the efficiency of the dorsoventral oscillations required of the swimming neonate. The m. intertransversarius caudae dorsalis (IT) is the most laterally placed epaxial muscle. Bilateral contractions of the IT could limit lateral deformations of the flexible tailstock of the early neonate. We test the hypothesis that the IT is functioning as a postural muscle in neonates by examining its morphological, histological and biochemical properties. The neonatal IT has a relatively large cross-sectional area and bending moment, as well as a large proportion of slow-twitch fibres and elevated myoglobin concentrations. Our results demonstrate that the IT is functionally capable of performing this specific postural function in neonatal dolphins. In later life-history stages, when postural control is no longer needed, the IT serves to fine-tune the position of the tailstock during locomotion. The changing function of the adult IT is concomitant with changes in morphology and biochemistry, and most notably, with an increase in the proportion of fast-twitch fibres. We suggest that these changes reflect strong selective pressure to improve locomotor abilities by limiting lateral deformations during this critical life-history stage.