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FIGURE 9 in Redescription and expansion of the geographic distribution of Phenacorhamdia nigrolineata (Siluriformes: Heptapteridae)
FIGURE 9 | Dispersion of individual scores of first two principal component analysis of four populations of Phenacorhamdia nigrolineata (blue dots = Ucayali River basin; brown dots = Amayacu River basin; green dots = Madeira River basin; black dots = Tapajós River basin), P. boliviana (gray dots = Beni River basin), and P. unifasciata (purple dots = Upper Paraná River basin).
FIGURE 8 in Redescription and expansion of the geographic distribution of Phenacorhamdia nigrolineata (Siluriformes: Heptapteridae)
FIGURE 8 | Geographical distribution of Phenacorhamdia nigrolineata in the western Amazon basin. Black star represents the type locality in Peru; black dots represent remaining known localities. One dot may represent more than one lot.
FIGURE 4 in Redescription and expansion of the geographic distribution of Phenacorhamdia nigrolineata (Siluriformes: Heptapteridae)
FIGURE 4 | Illustration of the cranium of Phenacorhamdia nigrolineata, dorsal view, MCP 53512, 40.0 mm SL. Abbreviations: af, anterior fontanel; AN, antorbital; AP, autopalatine; EP, epioccipital; ES, extrascapula; EX, exoccipital; FR, frontal; i1–6, infraorbital sensory branches 1 to 6; LE, lateral ethmoid; ME, mesethmoid; MX, maxilla; NA, nasal; pf, posterior fontanel; PRE, premaxilla; PT, pterotic; s1–8, supraorbital sensory branches 1 to 8; s2+i2) supraorbital sensory branch 2 + infraorbital sensory branch 2; SP, sphenotic; SOC, supraoccipital; SOCP, supraoccipital process. Scale bars = 1 mm.
Data from: Lineage-specific trait variations and plasticity of obligate parthenogenetic animals following the expansion of distribution range to a continental archipelago.
<p><span>Two asexual lineages, JPN1 and JPN2, of panarctic <em>Daphnia pulex</em> expanded the distribution range to Japan from North America, independent of each other. According to the mutation rates within these lineages, JPN1 lineage colonized Japan earlier than JPN2 lineage. Moreover, the ratio of nonsynonymous to synonymous mutation rates (dN/dS) was lower in JPN1 than in JPN2 lineage.</span></p> <p><span>Accordingly, it is hypothesized that variations of phenotypic traits differ between these two lineages. In addition, since they are obligate parthenogenetic animals, the lineage occupying a larger distribution range should have a larger phenotypic plasticity. To test these hypotheses, we experimentally examined the phenotypic variations of fitness-related traits, including digestive, life history and morphological traits, among several genotypes of these lineages.</span></p> <p><span>We found that within-lineage variations of most traits were smaller in JPN1 than in JPN2. In addition, the overall phenotypic variations were also smaller within the JPN1 lineage than within the JPN2 lineage. These results support the idea that the JPN1 lineage has been more efficiently subjected to negative selection, as expected from the lower dN/dS ratio.</span></p> <p><span>However, the magnitude of the phenotypic plasticity to changing food levels was at the same level for both the JPN1 and JPN2 lineages, while variations found in the phenotypic plasticity were smaller in the JPN1 lineage. The difference in the variations of the phenotypic traits and plasticity between the two lineages suggests that these two lineages have evolved under somewhat different environmental conditions and that genotypes of the JPN2 lineage may have exploited niches that differed somewhat from that of the JPN1 genotypes.</span></p>
WorldClim, elevation and distribution data for all palms from: The ecology of palm genomes: Repeat-associated genome size expansion is constrained by aridity
<p>Genome size varies 2,400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat 'communities' are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective.</p> <p>We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically-informed linear models to explore relationships between repeat dynamics and environmental factors.</p> <p>We show that palm genome size and repeat 'community' composition are best explained by aridity. Specifically, <em>Ty3-gypsy</em> and <em>TIR </em>elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. In contrast, <em>Ty1-copia</em> and <em>LINE </em>elements were more abundant in drier environments.</p> <p>Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements which may associate with stress-response genes (e.g., <em>Ty1-copia</em>) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat 'communities'. </p>
Population expansion, divergence, and persistence in western fence lizards (Sceloporus occidentalis) at the northern extreme of their distributional range
<p>Population dynamics within species at the edge of their distributional range, including the formation of genetic structure during range expansion, are difficult to study when they have had limited time to evolve. Western Fence Lizards (<em>Sceloporus occidentalis</em>) have a patchy distribution at the northern edge of their range around the Puget Sound, Washington, where they almost exclusively occur on imperiled coastal habitats. The entire region was covered by Pleistocene glaciation as recently as 16,000 years ago, suggesting that populations must have colonized these habitats relatively recently. We tested for population differentiation across this landscape using genome-wide SNPs and morphological data. A time-calibrated species tree supports the hypothesis of a post-glacial establishment and subsequent population expansion into the region. Despite a strong signal for fine-scale population genetic structure across the Puget Sound with as many as 8–10 distinct subpopulations supported by the SNP data, there is minimal evidence for morphological differentiation at this same spatiotemporal scale. Historical demographic analyses suggest that populations expanded and diverged across the region as the Cordilleran Ice Sheet receded. Population isolation, lack of dispersal corridors, and strict habitat requirements are the key drivers of population divergence in this system. These same factors may prove detrimental to the future persistence of populations as they cope with increasing shoreline development associated with urbanization.</p>
The confluence of traits and environmental factors driving diversification and niche expansion in the globally distributed order Myrtales
<p>Supplementary files for the article: <strong>The confluence of traits and environmental factors driving diversification and niche expansion in the globally distributed order Myrtales</strong></p>
Liolophura species discrimination with geographical distribution patterns and their divergence and expansion history on the northwestern Pacific coast
<p>Please refer to Choi et al. (2021): "Choi, E.H., Yeo, M.Y., Kim, G. <i>et al.</i> <i>Liolophura</i> species discrimination with geographical distribution patterns and their divergence and expansion history on the northwestern Pacific coast. <i>Sci Rep</i> <b>11, </b>17602 (2021).</p> <p>The chiton <em>Liolophura japonica</em> (Lischke, 1873) is widely distributed in intertidal coastal areas of the northwestern Pacific. Here we show species discrimination of <em>L. japonica</em> into two species and one subspecies based on <em>COI</em> and <em>16S rRNA</em>;<em> L. koreana</em>, sp. nov. was mainly distributed at ca. 33°24'–38°32' N, <em>L. japonica</em> at ca. 33°24'–35°53' N, and <em>L. j. sinensis</em>, ssp. nov. at ca. 27°02'–28°00' N. These species were morphologically distinguishable by black spots on the tegmentum and the shape of spicules on the perinotum. In addition, we have discussed their molecular divergence times (3.37 mya for<em> L. koreana </em>and<em> L. japonica</em>, around the mid Pliocene warm period; 1.84 mya for <em>L. japonica </em>and <em>L. j. sinensis</em>), demographic expansion events following the last interglacial age, called the Eemian (129–116 kya), and augmentation of <em>COI</em> haplotype diversity during the late-middle to late Pleistocene. Their latitudinal geographical distribution gradients may be helpful for monitoring the migration of marine 38 invertebrates north, fostered by global warming in the northwestern Pacific.</p>
Data from: Wallace 2: A shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions
<p>These are the occurrence locality datasets used in the example provided in "<em>wallace</em> 2: a <em>shiny</em> app for modeling species niches and distributions redesigned to facilitate expansion via module contributions" published in Ecography (DOI: 10.1111/ecog.06547). The analysis workflow is displayed in the Supporting information of the paper (Fig. S1), and these data are also used in the <em>wallace</em> 2 vignette (<a href="https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html">https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html</a>).</p>
Data from: Wallace 2: A shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions
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WorldClim, elevation and distribution data for all palms from: The ecology of palm genomes: Repeat-associated genome size expansion is constrained by aridity
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Data from: Lineage-specific trait variations and plasticity of obligate parthenogenetic animals following the expansion of distribution range to a continental archipelago.
Open the record for dataset details and reuse information.
Population expansion, divergence, and persistence in western fence lizards (Sceloporus occidentalis) at the northern extreme of their distributional range
Open the record for dataset details and reuse information.
Liolophura species discrimination with geographical distribution patterns and their divergence and expansion history on the northwestern Pacific coast
Open the record for dataset details and reuse information.
Trait variation, trade-offs, and attributes may contribute to colonization and range expansion of a globally distributed weed
Premise of the study Trait variation, trade-offs, and attributes can facilitate colonization and range expansion. We explored how those trait features compare between ancestral and non-native populations of the globally distributed weed Centaurea solstitialis. Methods We measured traits related to survival, size, reproduction, and dispersal in field sampling following major environmental gradients; that of elevation in Anatolia (ancestral range) and that of precipitation in Argentina (non-native range). We also estimated abundance. Key results We found that overall variation in traits in ancestral populations was similar to that in non-native populations. Only one trait, seed mass, displayed greater variation in ancestral than non-native populations; coincidentally, seed mass has been shown to track global range expansion of C. solstitialis. Traits displayed several associations, among which seed mass and number were positively related in both ranges. Many traits varied with elevation in the ancestral range, whereas none varied with precipitation in the non-native one. Interestingly, most traits varying with elevation within the ancestral range also displayed differences in attributes between ancestral and non-native ranges. Unexpectedly, ancestral plants were more fecund than non-native plants, but density was greater in the non-native than ancestral range, indicating that C. solstitialis survives at larger proportions in the non-native than ancestral range. Conclusions Our results suggest that maintaining levels of trait variation in non-native populations comparable to those in ancestral populations, avoiding trait trade-offs, and developing differences in trait attributes between ranges can play a major role in the success of many weeds in novel environments.
Data from: How do cold-adapted plants respond to climatic cycles? interglacial expansion explains current distribution and genomic diversity in Primula farinosa L.
Understanding the effects of past climatic fluctuations on the distribution and population-size dynamics of cold-adapted species is essential for predicting their responses to ongoing global climate change. In spite of the heterogeneity of cold-adapted species, two main contrasting hypotheses have been proposed to explain their responses to Late Quaternary glacial cycles, namely, the interglacial contraction versus the interglacial expansion hypotheses. Here, we use the cold-adapted plant Primula farinosa to test two demographic models under each of the two alternative hypotheses and a fifth, null model. We first approximate the time and extent of demographic contractions and expansions during the Late Quaternary by projecting species distribution models across the last 72 ka. We also generate genome-wide sequence data using a Reduced Representation Library approach to reconstruct the spatial structure, genetic diversity, and phylogenetic relationships of lineages within P. farinosa. Finally, by integrating the results of climatic and genomic analyses in an Approximate Bayesian Computation framework, we propose the most likely model for the extent and direction of population-size changes in P. farinosa through the Late Quaternary. Our results support the interglacial expansion of P. farinosa, differing from the prevailing paradigm that the observed distribution of cold-adapted species currently fragmented in high altitude and latitude regions reflects the consequences of postglacial contraction processes.
Data from: Unravelling the effects of contemporary and historical range expansion on the distribution of genetic diversity in the damselfly Coenagrion scitulum
Although genetic diversity provides the basic substrate for evolution, there are a limited number of studies that assess the impact of recent climate change on intraspecific genetic variation. This study aims to unravel the degree to which historical and contemporary factors shape genetic diversity and structure across a large part of the range of the range-expanding damselfly Coenagrion scitulum (Rambur, 1842). A total of 525 individuals from 31 populations were genotyped at nine microsatellites, and a subset was sequenced at two mitochondrial genes. We inferred the importance of geography, environmental factors, and recent range expansion on genetic diversity and structure. Genetic diversity decreased going westwards, suggesting a signature of historical post-glacial expansion from east to west and the presence of eastern refugia. Although genetic differentiation decreased going northwards, it increased in the northern edge populations, suggesting a role of contemporary range expansion on the genetic make-up of populations. The phylogeographical context was proven to be essential in understanding and identifying the genetic signatures of local contemporary processes. Within this framework, our results highlight that recent range expansion of a good disperser can decrease genetic diversity and increase genetic differentiation which should be considered when devising suitable conservation strategies.
Data from: Persistence with episodic range expansion from the early Pleistocene: the distribution of genetic variation in the forest tree Corymbia calophylla (Myrtaceae) in south-western Australia
Phylogeographic patterns of trees in topographically subdued, unglaciated landscapes are under-reported, and might reflect population persistence and the influences of environment and distance over historical (~2.6Mya-present) and contemporary (recent generations) time-scales. We examined this hypothesis using genetic analyses of four slowly evolving non-coding chloroplast sequences and 16 nuclear microsatellites in the tree Corymbia calophylla from south-western Australia that has been unglaciated since the Permian (.300-250Mya). We found strong population differentiation for chloroplast DNA and low differentiation for nuclear loci, consistent with higher gene flow by pollen than seed. We identified three divergent chloroplast lineages distributed in central, north and south geographic regions, and diversifying from the early (.3.028Mya), mid- (.0.793Mya) and late- (.0.426Mya) Pleistocene, respectively. Moderate-high nucleotide diversity with population-specific haplotypes supported long-term persistence but diversification of lineages provided evidence of unexpected episodic range expansion. We suggest this pattern reflects environmental influences of climatic oscillations during progressive drying of south-western Australia from the early Pleistocene. Significant tests for isolation by environment for nuclear loci also supported an influence of contemporary environmental (aridity) conditions on genetic structure, but isolation by distance (IBD) was greater. Significant chloroplast and nuclear IBD suggested distance was a major influence on gene flow at both time-scales.
Data from: Stepping-stone expansion and habitat loss explain a peculiar genetic structure and distribution of a forest insect
It is challenging to unravel the history of organisms with highly scattered populations. Such species may have fragmented distributions because extant populations are remnants of a previously more continuous range, or because the species has narrow habitat requirements in combination with good dispersal capacity (naturally or vector borne). The northern pine processionary moth Thaumetopoea pinivora has a scattered distribution with fragmented populations in two separate regions, northern and south-western Europe. The aims of this study were to explore the glacial and postglacial history of T. pinivora, and add to the understanding of its current distribution and level of contemporary gene flow. We surveyed published records of its occurrence and analysed individuals from a representative subset of populations across the range. A 633 bp long fragment of the mtDNA COI gene was sequenced and nine polymorphic microsatellite loci were genotyped. Only nine nucleotide sites were polymorphic in the COI gene and 90% of the individuals from across its whole range shared the same haplotype. The microsatellite diversity gradually declined towards the north, and unique alleles were found in only three of the northern and three of southern sites. Genetic structuring did not indicate complete isolation among regions, but an increase of genetic isolation by geographic distance. Approximate Bayesian model choice suggested recent divergence during the postglacial period, but glacial refugia remain unidentified. The progressive reduction of suitable habitats is suggested to explain the genetic structure of the populations and we suggest that T. pinivora is a cold-tolerant relict species, with situation-dependent dispersal.
Data from: Genetic constraints of population expansion of the Carpathian lynx at the western edge of its native distribution range in Central Europe
Even though populations of many large carnivores are expanding throughout Europe, the Eurasian lynx population in the Western Carpathians seems unable to spread beyond the western boundaries of its current distributional range. Many factors, both extrinsic and intrinsic, can influence the potential for range expansion: landscape fragmentation, natal philopatry, low natural fecundity and high mortality, and low and sex-biased dispersal rates. In this study we used non-invasive genetic sampling to determine population size fluctuation, sub-structuring and social organisation of the peripheral lynx population at the Czech-Slovak border. Even though the population size has been relatively stable over the period studied (2010-2016), the individual inbreeding coefficients of residents at the end of the study were much higher than those of founders at the beginning of the study. While non-resident individuals (predominantly males) occurred regularly in the study population, only resident individuals with well-established home ranges participated in breeding and produced offspring. Almost half the offspring detected in the study (predominantly females) settled in or near the natal area. Subsequent incestuous mating resulted in production of inbred individuals, reduction of effective population size of the population, and sub-structuring of the population through formation of two distinct family lineages. Our study illustrates how social constraints, such as territoriality, breeding of residents and natal philopatry of females lead to incestuous mating in small-sized populations, especially at the periphery of their distribution. This threat should be taken into account in planning of conservation and population recovery of species with similar social structure.
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