Comparative Phylogeography in Fijian Coral Reef Fishes: A Multi-Taxa Approach towards Marine Reserve Design

Delineating barriers to connectivity is important in marine reserve design as they describe the strength and number of connections among a reserve''s constituent parts, and ultimately help characterize the resilience of the system to perturbations at each node. Here we demonstrate the utility of multi-taxa phylogeography in the design of a system of marine protected areas within Fiji. Gathering mtDNA control region data from five species of coral reef fish in five genera and two families, we find a range of population structure patterns, from those experiencing little (Chrysiptera talboti, Halichoeres hortulanus, and Pomacentrus maafu), to moderate (Amphiprion barberi, Φ_st = 0.14 and Amblyglyphidodon orbicularis Φ_st = 0.05) barriers to dispersal. Furthermore estimates of gene flow over ecological time scales suggest species-specific, asymmetric migration among the regions within Fiji. The diversity among species-specific results underscores the limitations of generalizing from single-taxon studies, including the inability to differentiate between a species-specific result and a replication of concordant phylogeographic patterns, and suggests that greater taxonomic coverage results in greater resolution of community dynamics within Fiji. Our results indicate that the Fijian reefs should not be managed as a single unit, and that closely related species can express dramatically different levels of population connectivity.     

The importance of turtle populations to wetland restoration in the Upper Mississippi Embayment of the Mississippi Alluvial Valley

Wetlands Ecology and Management - The Upper Mississippi Embayment (UME) ecoregion covers approximately 141,895 km2 and historically supported 9,712,455 ha of bottomland...     

Comparative Microhabitat Use of Ecologically Similar Benthic Fishes

Although benthic insectivorous fishes such as darters and sculpins represent a significant component of riffle communities, few studies have compared the habitat use of these non-related but ecologically similar fishes. The objectives of this study were to examine the habitat use of Etheostoma olmstedi (tessellated darter) compared to Cottus bairdi (mottled sculpin) in Nescopeck Creek and Cottus cognatus (slimy sculpin) in Jack's Creek, Pennsylvania through underwater observation. Etheostoma olmstedi occupied habitats with significantly deeper waters than those available, whereas adult and young of the year Cottus occupied habitats with significantly faster water velocities than those available. Canonical discriminant analysis revealed microhabitat partitioning between E. olmstedi and each Cottus species. Cottus bairdi and C. cognatus occupied significantly shallower habitats with faster water velocities than E. olmstedi. Sculpin species were observed most frequently under substrate whereas E. olmstedi occurred most frequently on the top surface of the substrate. Hurlbert's standardized niche breadth values indicated that C. bairdi and C. cognatus were habitat specialists with regard to water velocity measures, but exhibited generalistic patterns of depth and substrate size use. Etheostoma olmstedi was a habitat specialist with respect to depth, but exhibited generalistic patterns of resource use for substrate size. Differential habitat use by these benthic fishes is consistent with the hypothesis that resource partitioning facilitates species coexistence among stream fishes.     

Comparative Phylogeography in Rainforest Trees from Lower Guinea,Africa

Comparative phylogeography is an effective approach to assess the evolutionary history of biological communities. We used comparative phylogeography in fourteen tree taxa from Lower Guinea (Atlantic Equatorial Africa) to test for congruence with two simple evolutionary scenarios based on physio-climatic features 1) the W-E environmental gradient and 2) the N-S seasonal inversion, which determine climatic and seasonality differences in the region. We sequenced the trnC-ycf6 plastid DNA region using a dual sampling strategy: fourteen taxa with small sample sizes (dataset 1, mean n = 16/taxon), to assess whether a strong general pattern of allele endemism and genetic differentiation emerged; and four taxonomically well-studied species with larger sample sizes (dataset 2, mean n = 109/species) to detect the presence of particular shared phylogeographic patterns. When grouping the samples into two alternative sets of two populations, W and E, vs. N and S, neither dataset exhibited a strong pattern of allelic endemism, suggesting that none of the considered regions consistently harboured older populations. Differentiation in dataset 1 was similarly strong between W and E as between N and S, with 3–5 significant F _ST tests out of 14 tests in each scenario. Coalescent simulations indicated that, given the power of the data, this result probably reflects idiosyncratic histories of the taxa, or a weak common differentiation pattern (possibly with population substructure) undetectable across taxa in dataset 1. Dataset 2 identified a common genetic break separating the northern and southern populations of Greenwayodendron suaveolens subsp. suaveolens var. suaveolens, Milicia excelsa, Symphonia globulifera and Trichoscypha acuminata in Lower Guinea, in agreement with differentiation across the N–S seasonal inversion. Our work suggests that currently recognized tree taxa or suspected species complexes can contain strongly differentiated genetic lineages, which could lead to misinterpretation of phylogeographic patterns. Therefore the evolutionary processes of such taxa require further study in African tropical rainforests.     

2种珍稀裂腹鱼类线粒体DNA部分序列片段的比较分析

对扁吻鱼(Aspiorhynchus laticeps)及塔里木裂腹鱼(Schizothorax biddulphi)线粒体CO I(624 bp)、Cyt b(712 bp)和D-loop(457 bp)基因片段进行了PCR扩增和序列测定.通过分析比较发现,3个片段A+T含量与其他鱼类相比均较高,G含量偏低这一现象在...     

Comparative Phylogeography of Mesoamerican Highland Rodents: Concerted versus Independent Response to Past Climatic Fluctuations

The phylogeography of Sumichrast's harvest mouse (Reithrodontomys sumichrasti) was examined through maximum-likelihood and parsimony analyses of 1,130 bp of mitochondrial Cytochrome b sequence data from 43 individuals. The phylogeography of this Middle American highland forest-dwelling species was compared to that previously published for the codistributed Aztec deer mouse complex (Peromyscus aztecus/Peromyscus hylocetes complex) in order to test competing hypotheses of concerted versus independent responses of codistributed forms to past climatic fluctuations. Qualitatively, there were strong similarities in the phylogeographic patterns of the two groups, yet there were also areas of incongruence. Likelihood-ratio tests (Kishino-Hasegawa-Templeton and parametric bootstrap tests) indicated that this incongruence is significant and cannot be attributed simply to uncertainty in phylogenetic estimation, thereby falsifying the concerted-response hypothesis. Conversely, tree-reconciliation analysis of the area relationships inferred for each group separately indicated that there has been a significant history of covicariance between the two groups, falsifying the independent-response hypothesis. It appears that codistributed taxa in the geologically complex highlands of Mesoamerica share more common biogeographical history than can be accounted for by the independent-response hypothesis yet have not responded to past climatic fluctuations in the lock-step fashion predicted by the concerted-response hypothesis.     

A Comparative Analysis of Morphofunctional Characteristics of Cartilaginous Ganoid Fishes (Order Chondrostei)

Journal of Evolutionary Biochemistry and Physiology - The review article provides a comparative analysis of the morphological and functional characteristics of cartilaginous ganoid fishes...     

Comparative breeding ecology of Mississippi Kites in urban and exurban areas of West Texas

Birds of prey are becoming increasingly common occupants of urbanized settings, but the comparative benefits or detriments they experience in urban environs compared to exurban areas are poorly understood. We examined the reproductive success and phenology of Mississippi Kites (Ictinia mississippiensis) nesting concurrently in urban and exurban areas in west Texas during the 2010–2012 and 2014 breeding seasons. Our objective was to better understand the reproductive advantages or disadvantages that kites may experience by nesting in urban areas rather than exurban areas. We calculated annual productivity, estimated daily survival rates of nests, and estimated hatch dates. Kites produced 0.52 fledglings per urban nesting attempt and 0.33 fledglings per exurban nesting attempt. We found no difference in the mean number of young that fledged from successful urban (1.06) and exurban (1.07) nests, but kites in urban areas had greater nesting success within years than those in exurban areas. Both heat and drought were associated with low productivity and success in both areas, but the urban landscape appears to have provided some buffer to their effects. These factors may have had direct (e.g., exposure) or indirect (e.g., negative influences on prey availability) influences on reproductive success. Counter to previous studies of urban raptors, we found that exurban kites nested significantly earlier than urban kites. This may be linked to differences in environmental conditions and prey availability between the areas. Our results suggest that urban areas provide a reproductive advantage for Mississippi Kites in terms of facilitating an overall higher nesting success, but this does not translate into increased productivity for successful pairs. Further, our data suggest that, although urban areas may buffer species from drought or heat, that buffer can be breached during severe conditions.     

Comparative Phylogeography Highlights the Double-Edged Sword of Climate Change Faced by Arctic- and Alpine-Adapted Mammals

Recent studies suggest that alpine and arctic organisms may have distinctly different phylogeographic histories from temperate or tropical taxa, with recent range contraction into interglacial refugia as opposed to post-glacial expansion out of refugia. We use a combination of phylogeographic inference, demographic reconstructions, and hierarchical Approximate Bayesian Computation to test for phylodemographic concordance among five species of alpine-adapted small mammals in eastern Beringia. These species (Collared Pikas, Hoary Marmots, Brown Lemmings, Arctic Ground Squirrels, and Singing Voles) vary in specificity to alpine and boreal-tundra habitat but share commonalities (e.g., cold tolerance and nunatak survival) that might result in concordant responses to Pleistocene glaciations. All five species contain a similar phylogeographic disjunction separating eastern and Beringian lineages, which we show to be the result of simultaneous divergence. Genetic diversity is similar within each haplogroup for each species, and there is no support for a post-Pleistocene population expansion in eastern lineages relative to those from Beringia. Bayesian skyline plots for four of the five species do not support Pleistocene population contraction. Brown Lemmings show evidence of late Quaternary demographic expansion without subsequent population decline. The Wrangell-St. Elias region of eastern Alaska appears to be an important zone of recent secondary contact for nearctic alpine mammals. Despite differences in natural history and ecology, similar phylogeographic histories are supported for all species, suggesting that these, and likely other, alpine- and arctic-adapted taxa are already experiencing population and/or range declines that are likely to synergistically accelerate in the face of rapid climate change. Climate change may therefore be acting as a double-edged sword that erodes genetic diversity within populations but promotes divergence and the generation of biodiversity.     

Late Cretaceous marine arthropods relied on terrestrial organic matter as a food source: Geochemical evidence from the Coon Creek Lagerstätte in the Mississippi Embayment

The Upper Cretaceous Coon Creek Lagerstätte of Tennessee, USA, is known for its extremely well‐preserved mollusks and decapod crustaceans. However, the depositional environment of this unit, particularly its distance to the shoreline, has long been equivocal. To better constrain the coastal proximity of the Coon Creek Formation, we carried out a multiproxy geochemical analysis of fossil decapod (crab, mud shrimp) cuticle and associated sediment from the type section. Elemental analysis and Raman spectroscopy confirmed the presence of kerogenized carbon in the crabs and mud shrimp; carbon isotope (δ¹³C) analysis of bulk decapod cuticle yielded similar mean δ¹³C values for both taxa (?25.1‰ and ?26‰, respectively). Sedimentary biomarkers were composed of n‐alkanes from C₁₆ to C₃₆, with the short‐chain n‐alkanes dominating, as well as other biomarkers (pristane, phytane, hopanes). Raman spectra and biomarker thermal maturity indices suggest that the Coon Creek Formation sediments are immature, which supports retention of unaltered, biogenic isotopic signals in the fossil organic carbon remains. Using our isotopic results and published calcium carbonate δ¹³C values, we modeled carbon isotope values of carbon sources in the Coon Creek Formation, including potential marine (phytoplankton) and terrestrial (plant) dietary sources. Coon Creek Formation decapod δ¹³C values fall closer to those estimated for terrigenous plants than marine phytoplankton, indicating that these organisms were feeding primarily on terrigenous organic matter. From this model, we infer that the Coon Creek Formation experienced significant terrigenous organic matter input via a freshwater source and thus was deposited in a shallow, nearshore marine environment proximal to the shoreline. This study helps refine the paleoecology of nearshore settings in the Mississippi Embayment during the global climatic shift in the late Campanian–early Maastrichtian and demonstrates for the first time that organic δ¹³C signatures in exceptionally preserved fossil marine arthropods are a viable proxy for use in paleoenvironmental reconstructions.     

Adaptations of Cave Fishes with some Comparisons to Deep-sea Fishes

I provide my retrospective and prospective views on adaptations of cave fishes. I emphasize the history of my insights into cave adaptation from 45 years of research using surface, cave-spring, and cave species of amblyopsid fishes. My approach has been to use natural experiments and to always consider multiple hypotheses. To clarify evolutionary adaptations, I show the importance of a broad comparative approach which includes studies of morphology, metabolic physiology, foraging behavior, life history, and ecology. And I show that the most important agents of selection, of darkness and attendant low food supply, are best understood in the context of rigor, variability, and predictability. I also present my insights from what I consider the most insightful contributions on deep-sea fishes. The contributions are those of Marshall in studies of morphology in relation to energy economy of pelagic and benthic species, Childress in studies of physiological and biochemical adaptations with depth for pelagic species, and Koslow in studies on population biology and life history of bathybenthic and benthic sea-mount species. Compared to caves, I suggest that the extremes of metabolic and life history adaptations of deep-sea fish are explained by a longer evolutionary history and a much greater habitat range, food supply, and predation risk. Finally, I take a retrospective view of what we have learned about cave fishes. I discuss possible evolutionary mechanisms that can explain the trends with increasing cave adaptation in amblyopsid fishes, especially progenesis and the pleiotropic effects of the stress resistance syndrome. Finally, based on insights from deep-sea fishes, and emerging new techniques, I suggest what cave fish biologists should do in the future.     

Morphological and molecular variation in the least madtom Noturus hildebrandi (Siluriformes: Ictaluridae), a Mississippi Embayment endemic: evidence for a cryptic lineage in the Hatchie River

Sheared principal component analysis of 40 morphometric characteristics measured for 146 individuals and relative frequencies of pigmentation patterns scored for 980 individuals of the least madtom Noturus hildebrandi, a diminutive catfish endemic to eastern lowland drainages of the Mississippi Embayment region of North America, suggested a clinal pattern of morphological variation extending across the range from north to south. DNA sequence data representing 90 individuals from the mitochondrial gene cytochrome b (cytb) analysed using Bayesian phylogenetic methods recovered four major haplotype clades, suggestive of a high degree of isolation by drainage. Individual gene trees of cytb and four additional nuclear loci as well as trees based on concatenated datasets of these genes consistently recovered a cryptic lineage of individuals from the Hatchie River drainage that is morphologically indistinguishable from surrounding populations. Gene‐tree analyses failed to recover a monophyletic N. hildebrandi with respect to Noturus baileyi. A coalescence‐based species tree analysis, however, did recover N. hildebrandi monophyly with high support, suggesting that relationships reflected in individual gene trees and concatenated datasets are in part artefacts of incomplete lineage sorting or an ancient introgressive event. Results are consistent with the hypothesis of an ancient connection between the Hatchie and Tennessee River systems. Current subspecific designations are of limited utility as they reflect morphological variation and are not entirely consistent with phylogeny. Discrepancies between the pattern of variation observed in the morphological and molecular data may be explained by recent local adaptation to individual stream conditions that masks deeper evolutionary divergences.     

数种鱼类肌肉中氨基酸成分及含量的比较研究

综述了１２科２９种鱼类肌肉氨基酸成分及含量。结果表明,鱼类肌肉氨基酸种类齐全,约１７－２０种;总氨基酸含量较高,占９．６２－９３．６０％,其中必需氨基酸储量丰富,占总氨基酸含量的３７．７５－５８．４４％。通过比较发现乌鳢、团头鲂、矛尾复虾虎鱼、鳙、鲤和虹鳟等６种鱼类肌肉氨基酸总量高于其他２３种鱼类,确为鱼中佳品。     

Phylogeography and marine retention

A number of studies now point to the association of patterns of phylogeography with discontinuities in coastal current patterns. If such phylogeographic patterns are indicative of populations that retain local diversity, as has been predicted by recent modelling, such results may be of use in marine reserve planning. Here we show that there is a distributional correlation on the Pacific coast of North America between marine reserve placement and phylogeographic patterns. A number of factors could contribute to this correlation, but its existence suggests the utility of genetic studies in marine conservation planning.     

Reproductive Physiology of Fishes

Atlantic cod Gadus morhua larvae reached four‐fold (at low larval density) to 11 fold higher body mass (high larval density) at 50 days post hatch (dph) when fed zooplankton rather than enriched rotifers. A short period (22–36 dph) of dietary change affected larval growth positively if changed from enriched rotifers to natural zooplankton and negatively if prey type changed vice versa. Overall survival did not differ between the two larval groups at low larval density, but at high density the rotifer group had a higher overall survival (10·8% v. 8·9%). Long‐term growth was affected significantly by larval diet in favour of the zooplankton diet; juveniles reached a 23% higher mass in a 12 week growth period. No difference in growth performance was found between juveniles fed natural zooplankton during the larval period for 36, 22 or 14 days, but all these juveniles performed significantly better compared with the rotifer‐fed group. These findings suggest that optimal diet during a short period in the larval period can result in improved growth in both the larval and juvenile period. Improved rotifer quality may, therefore, hold a large potential for growth improvement in this species.