cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.47d7wm38v
title: Data from: Step-patterned survivorship curves: mortality and loss of equilibrium responses to high temperature and food restriction in juvenile rainbow trout (Oncorhynchus mykiss)

description: While survivorship curves typically exhibit smooth declines over time,
 step-patterned curves can occur with multiple stressors within a life
 stage. To explore this process, we examined the effects of heat (24 ºC)
 and food restriction on juvenile rainbow trout (Oncorhynchus mykiss
 Walbaum) in challenge experiments. We observed step-patterned survivorship
 curves determined by mortality and loss of equilibrium (LOE) endpoints. To
 examine the cause of heterogeneity in the stress responses from early to
 late mortality and LOE, we measured indices of energetic reserves. The
 step transition in the survivorship curves, the peak mortality rates, and
 start of when individuals reached a critical energetic threshold (14% dry
 mass; 4.0 kJ·g-1 energy) all occurred at around days 10-15 of the
 challenge. The coherence in these temporal patterns suggest heterogeneity
 in the cohort stress responses, in which an early subgroup died from heat
 stress and a late subgroup died from starvation. Thus, their endpoint
 sensitivities resulted in step-patterned survivorship curves. We discuss
 the implications of the study for understanding effects of multiple
 stressors on population heterogeneity and note the possible significance
 of stress response selection under climate change in which heat stress and
 food limitations occur in concert.
DOI: 10.5061/dryad.w0vt4b8ms
title: Gene flow and climate-associated genetic variation in a vagile habitat specialist

description: Previous work in landscape genetics suggests that geographic isolation is
 of greater importance to genetic divergence than variation in
 environmental conditions. This is intuitive when configurations of
 suitable habitat are the dominant factor limiting dispersal and gene flow,
 but has not been thoroughly examined for habitat specialists with strong
 dispersal capability. Here, we evaluate the effects of geographic and
 environmental isolation on genetic divergence in a vagile invertebrate
 with high habitat specificity and a discrete dispersal life stage: Dod’s
 Old World swallowtail butterfly, Papilio machaon dodi. In Canada, P. m.
 dodi are generally restricted to eroding habitat along major river valleys
 where their larval host plant occurs. A series of causal and linear mixed
 effects models indicate that divergence of genome-wide single nucleotide
 polymorphisms is best explained by a combination of environmental
 isolation (variation in summer temperatures) and geographic isolation
 (Euclidean distance). Interestingly, least-cost path and circuit distances
 through a resistance surface parameterized as the inverse of habitat
 suitability were not supported. This suggests that, although habitat
 associations of many butterflies are specific due to reproductive
 requirements, habitat suitability and landscape permeability are not
 equivalent concepts due to considerable adult vagility. We infer that
 divergent selection related to variation in summer temperatures has
 produced two genetic clusters within P. m. dodi, differing in voltinism
 and diapause propensity. Within the next century, temperatures are
 predicted to rise by amounts greater than the present-day difference
 between regions of genetic clusters, potentially affecting the persistence
 of the northern cluster under continued climate change.
DOI: 10.5061/dryad.rxwdbrv4g
title: Reproductive hormones mediate changes in the gut microbiome during pregnancy and lactation in Phayre’s leaf monkeys

description: Studies in multiple host species have shown that gut microbial diversity
 and composition change during pregnancy and lactation. However, the
 specific mechanisms underlying these shifts are not well understood. Here,
 we use longitudinal data from wild Phayre’s leaf monkeys to test the
 hypothesis that fluctuations in reproductive hormone concentrations
 contribute to gut microbial shifts during pregnancy. We described the
 microbial taxonomic composition of 91 fecal samples from 15 females (n=16
 cycling, n=36 pregnant, n=39 lactating) using 16S rRNA gene amplicon
 sequencing and assessed whether the resulting data were better explained
 by overall reproductive stage or by fecal estrogen (fE) and progesterone
 (fP) concentrations. Our results indicate that while overall reproductive
 stage affected gut microbiome composition, the observed patterns were
 driven by reproductive hormones. Females had lower gut microbial diversity
 during pregnancy and fP concentration was negatively correlated with
 diversity. Additionally, fP concentration predicted both unweighted and
 weighted UniFrac distances, while reproductive state only predicted
 unweighted UniFrac distances. Seasonality (rainfall and periods of
 phytoprogestin consumption) additionally influenced gut microbial
 diversity and composition. Our results indicate that reproductive
 hormones, specifically progestagens, contribute to the shifts in the gut
 microbiome during pregnancy and lactation.
DOI: 10.5061/dryad.pzgmsbcgf
title: Individual quality and extra-pair paternity in the blue tit: sexy males bear the costs

description: Adaptive explanations for the evolution of extra-pair paternity (EPP)
 suggest that females seek extra-pair copulations with high quality males.
 Still, the link between ornamentation, individual quality and paternity
 remains unclear. Moreover, honest signaling is essential when explaining
 EPP because it is needed for sexual selection to occur; yet, it is
 understudied in multiple ornaments. Because blue tits (Cyanistes
 caeruleus) show variable color expression in several plumage patches, we
 tested: (i) over two seasons, whether males in better condition, more
 ornamented and less infected by blood parasites gain EPP and have higher
 reproductive success, and (ii) over three seasons, whether mating patterns
 affect color change. Males with more saturated yellow feathers, brighter
 tails and in better condition had higher reproductive success in one of
 the seasons. Contrary to expectation, in another season, males that gained
 EPP were parasitized by blood parasites, suggesting increased vector
 exposure during extra-pair copulations. Our results for two seasons show
 that males siring more extra-pair young were older and grew brighter cheek
 or tail feathers for the following season. Despite the increased mating
 costs, in socially monogamous avian systems, high quality males incur in
 EPP without compromising traits that may be under sexual
 selection.
DOI: 10.5061/dryad.h9w0vt4dx
title: Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska

description: Larix laricina (eastern larch, tamarack) is a transcontinental North
 American conifer with a prominent disjunction in the Yukon isolating the
 Alaskan distribution from the rest of its range. We investigate whether in
 situ persistence during the Last Glacial Maximum (LGM) or long-distance
 postglacial migration from south of the ice sheets resulted in the
 modern-day Alaskan distribution. We analyzed variation in three
 chloroplast DNA regions of 840 trees from a total of 69 populations (24
 new sampling sites situated on both sides of the Yukon range disjunction
 pooled with 45 populations from a published source) and conducted ensemble
 species distribution modeling (SDM) throughout Canada and USA to hindcast
 the potential range of Larix laricina during the LGM. We uncovered the
 genetic signature of a long-term isolation of larch populations in Alaska,
 identifying three endemic chlorotypes and low levels of genetic diversity.
 Range-wide analysis across North America revealed the presence of a
 distinct Alaskan lineage. Postglacial gene flow across the Yukon divide
 was unidirectional, from Alaska toward previously glaciated Canadian
 regions, and with no evidence of immigration into Alaska. Hindcast SDM
 indicates one of broadest areas of past climate suitability for Larix
 laricina existed in central Alaska, suggesting possible in situ
 persistence of larch in Alaska during the LGM. Our results provide the
 first unambiguous evidence for the long-term isolation of Larix laricina
 in Alaska that extends beyond the last glacial period and into the present
 interglacial period. The lack of gene flow into Alaska along with the
 overall probability of larch occurrence in Alaska being currently lower
 than during the LGM, suggest that modern-day Alaskan larch populations are
 isolated climate relicts of broader glacial
 distributions, and so are particularly vulnerable to
 current warming trends.
DOI: 10.5061/dryad.cnp5hqc1t
title: Climate change, sex reversal, and lability of sex determining systems

description: Sex reversal at high temperatures during embryonic development (e.g. ZZ
 females) provides the opportunity for new genotypic crosses (e.g. ZZ male
 x ZZ female). This raises the alarming possibility that climatic warming
 could lead to the loss of an entire chromosome – one member of the sex
 chromosome pair (the Y or W) – and the transition of populations to
 environmental sex determination (ESD). Here we examine the evolutionary
 dynamics of sex-determining systems exposed to climatic warming using
 theoretical models. We found that the loss of sex chromosomes is not an
 inevitable consequence of sex reversal. A large frequency of ZZ sex
 reversal (50% reversal from male to female) typically divides the outcome
 between loss of the ZW genotype and the stable persistence of ZZ males, ZW
 females, and ZZ females. The amount of warming associated with sex
 chromosome loss depended on several features of wild populations –
 environmental fluctuation, immigration, heritable variation in temperature
 sensitivity, and differential fecundity of sex-reversed individuals.
 Chromosome loss was partially or completely buffered when sex-reversed
 individuals suffered a reproductive fitness cost, when immigration
 occurred, or when heritable variation for temperature sensitivity existed.
 Thus, under certain circumstances, sex chromosomes may persist cryptically
 in systems where the environment is the predominant influence on sex.
description: These data were generated from individual-based simulations of
 animal populations (initial population size = 500) coded in Matlab. Each
 row presents relevant parameter values for a single simulation as well as
 relevant final model output following 300 iterations.
description: Please refer to the publication for model structure and symbol
 definitions.
DOI: 10.5061/dryad.gxd2547gr
title: Evaluation of the silkworm lemon mutant as an invertebrate animal model for human sepiapterin reductase deficiency

description: Human sepiapterin reductase deficiency is an inherited disease caused by
 SPR gene mutations and is a monoamine neurotransmitter disorder.
 Here, we investigated whether the silkworm lemon mutant could
 serve as a model of sepiapterin reductase deficiency. A point
 mutation in the BmSPR gene led to a five amino acid deletion at
 the carboxyl terminus in the lemon mutant. In addition, classical
 phenotypes seen in sepiapterin reductase deficient patients were
 observed in the lemon mutant, including a normal phenylalanine
 level, a decreased dopamine and serotonin content, and
 an increased neopterin level. A recovery test showed that
 replenishment of L-dopa significantly increased the dopamine
 level in the lemon mutant. The silkworm lemon mutant also showed
 negative behavioral abilities. These results suggest that
 the silkworm lemon mutant has an appropriate genetic basis and
 meets the biochemical requirements to be a model of sepiapterin
 reductase deficiency. Thus, the silkworm lemon mutant can serve
 as a candidate animal model of sepiapterin reductase
 deficiency, which may be helpful in facilitating accurate
 diagnosis and effective treatment options of sepiapterin
 reductase deficiency.
description: The gene sequence and amino acid sequence used in the
 manuscript.
DOI: 10.5061/dryad.fttdz08p5
title: Causes of differences in the distribution of the invasive plants Ambrosia artemisiifolia and Ambrosia trifida in Yili Valley, China

description: Ambrosia artemisiifolia and Ambrosia trifida are two species of very
 harmful and invasive plants of the same genus. However, it remains unclear
 why A. artemisiifolia is more widely distributed than A. trifida
 worldwide. Distribution and abundance of these two species were surveyed
 and measured from 2010 to 2017 in the Yili Valley, Xinjiang, China. Soil
 temperature and humidity, main companion species, the biological
 characteristics in farmland ecotone, residential area, roadside and
 grassland, and water demand of the two species were determined and studied
 from 2017 to 2018. The area occupied by A. artemisiifolia in the Yili
 Valley was more extensive than that of A. trifida, while the abundance of
 A. artemisiifolia in grassland was less than that of A. trifida at eight
 years after invasion. The interspecific competitive ability of two species
 were stronger than those of companion species in farmland ecotone,
 residential, and roadside. In addition, A. trifida had greater
 interspecific competitive ability than other plant species in grassland.
 The seed size and seed weight of A. trifida were five times or eight times
 those of A.artemisiifolia. When comparing the changes under simulated
 annual precipitation of 840 mm versus 280 mm, the seed yield per m2 of A.
 trifida decreased from 50,185 to 19, while that of A. artemisiifolia
 decreased from 15,579 to 530. The differences in the distribution of the
 two species are mainly due to differences in interspecific competitive
 ability, seed size, and water dependence. The two species have stronger
 interspecific competitive ability than that of companion species, but A.
 artemisiifolia has a smaller seed size and stronger drought tolerance,
 which allows A. artemisiifolia to spread farther than A. trifida. The
 reason for wider distribution of A. trifida in grassland is that A.
 trifida has stronger interspecific competitive ability than A.
 artemisiifolia under sufficient water.
DOI: 10.6078/d1dm6g
title: Temporal dynamics of migration-linked genetic variation are driven by streamflows and riverscape permeability

description: The permeability of landscapes is often explored spatially, but may also
 vary across time. For example, highways are more passable with low
 traffic, and mountain landscapes are more passable once snow-free.
 Landscape permeability especially influences migratory animals. Partial
 barriers are features that are passable in some conditions. Partial
 barriers are common in rivers due to the two-dimensional nature of river
 networks: aquatic organisms cannot circumvent in-river barriers. Barriers
 in river networks include waterfalls, logjams, or culverts, all of which
 vary in permeability depending on streamflow. We explore the influence of
 partial barriers on the spatial and temporal distribution of
 migration-linked genotypes of fish in tributaries to the South Fork Eel
 River, California, USA. We study Oncorhynchus mykiss, a salmonid fish with
 co-occurring resident and migratory forms. We genotyped &gt;3,000
 individuals using RAD-capture and classified individuals as resident,
 heterozygous, or migratory-genotypes using life history-associated loci.
 Across four years of study (2014-2017), the permeability of partial
 barriers varied with streamflow, and the largest waterfall was passable
 4-39 days/year. In one stream, partial barriers limited the up-river
 movement of migratory adult fish, decreasing the number of migratory
 juveniles found upstream of barriers (67-76% of the total migratory
 alleles in the watershed were downstream of the largest barrier). In
 another stream, migratory allele frequencies varied from 30-68%. Our work
 highlights the temporal dynamics of landscape permeability, which
 influences animal movements and genotype frequencies. While temporal
 variation in landscape permeability is likely common, migratory animals
 may be especially affected in their movement and genetic structure.
description: See methods in associated paper, Kelson et al. Temporal dynamics
 of migration-linked genetic variation are driven by streamflows and
 riverscape permeability.
description: See "read me" files associated with each data
 file.
DOI: 10.5061/dryad.x3ffbg7f8
title: Nitrogen economy of alpine plants on the north Tibetan Plateau: nitrogen conservation by resorption rather than open sources through biological symbiotic fixation

description: Nitrogen (N) is one of the most important factors limiting plant
 productivity, and N fixation by legume species is an important source of N
 input into ecosystems. Meanwhile, N resorption from senescent plant
 tissues conserves nutrients taken up in the current season, which may
 alleviate ecosystem N limitation. N ﬁxation was assessed by the 15N
 dilution technique in four types of alpine grasslands along the
 precipitation and soil nutrient gradients. The N resorption efficiency
 (NRE) was also measured in these alpine grasslands. The aboveground
 biomass in the alpine meadow was 4–6 times higher than in the alpine
 meadow-steppe, alpine steppe, and alpine desert-steppe. However, the
 proportion of legume species to community biomass in the alpine steppe and
 the alpine desert steppe was significantly higher than the proportion in
 the alpine meadow. N fixation by the legume plants in the alpine meadow
 was 0.236 g N m-2, which was significantly higher than N fixation in other
 alpine grasslands (0.041 to 0.089 g N m-2). The NRE in the alpine meadows
 was lower than in the other three alpine grasslands. Both the aboveground
 biomass and N fixation of the legume plants showed decreasing trends with
 the decline of precipitation and soil N gradients from east to west, while
 the NRE of alpine plants showed increasing trends along the gradients,
 which indicates that alpine plants enhance the NRE to adapt to the
 increasing droughts and nutrient-poor environments. The opposite trends of
 N fixation and NRE along the precipitation and soil nutrient gradients
 indicate that alpine plants adapt to precipitation and soil nutrient
 limitation by promoting NRE (conservative nutrient use by alpine plants)
 rather than biological N fixation (open sources by legume plants) on the
 north Tibetan Plateau.
DOI: 10.5061/dryad.pvmcvdnh0
title: Early Silurian chondrichthyans from the Tarim Basin (Xinjiang, China)

description: The Sinacanthida ordo nov. and Mongolepidida are spine- and scale-based
 taxa whose remains encompass some of the earliest reported fossils of
 chondrichthyan fish. Investigation of fragmentary material from the Early
 Silurian Tataertag and Ymogantau Formations of the Tarim Basin (Xinjiang
 Uygur Autonomous Region, China) has revealed a diverse mongolepidid and
 sinacanthid fauna dominated by mongolepids and sinacanthids in association
 with abundant dermoskeletal elements of the endemic ‘armoured’ agnathans
 known as galeaspids. Micro-computed tomography, scanning electron
 microscopy and histological sections were used to identify seven
 mongolepid genera (including Tielikewatielepis sinensis gen. et sp. nov.,
 Xiaohaizilepis liui gen. et sp. nov. and Taklamakanolepis asiaticus gen.
 et sp. nov.) together with a new chondrichthyan (Yuanolepis bachunensis
 gen. et sp. nov.) with scale crowns consisting of a mongolepid-type
 atubular dentine (lamellin). Unlike the more elaborate crown architecture
 of mongolepids, Yuanolepis gen. nov. exhibits a single row of crown
 elements consistent with the condition reported in stem chondrichthyans
 from the Lower Devonian (e.g. in Seretolepis, Parexus). The results
 corroborate previous work by recognising lamellin as the main component of
 sinacanthid spines and point to corresponding developmental patterns
 shared across the dermal skeleton of taxa with lamellin and more derived
 chondrichthyans (e.g. Doliodus, Kathemacanthus, Seretolepis and Parexus).
 The Tarim mongolepid fauna is inclusive of coeval taxa from the South
 China Block and accounts for over two-thirds of the species currently
 attributed to Mongolepidida. This demonstrates considerable overlap
 between the Tarim and South China components of the Lower Silurian
 Zhangjiajie Vertebrate Fauna.
DOI: 10.5061/dryad.3bk3j9kfc
title: Dietary polyunsaturated fatty acids affect volume and metabolism of Drosophila melanogaster sperm

description: Dietary fatty acids can accumulate in sperm and affect their function in
 vertebrates. As Drosophila melanogaster shares several pathways of lipid
 metabolism and shows similar lipid-dependent phenotypes but lacks some
 hormones that in vertebrates regulate lipid metabolism, there is currently
 no clear prediction as to how dietary fatty acids affect the sperm of D.
 melanogaster. We manipulated the amount and identity of dietary
 polyunsaturated fatty acids (PUFA) in the food of D. melanogaster males (a
 treatment known to affect membrane fluidity) and measured changes in sperm
 parameters. We found that i) males reared on food containing PUFA-rich,
 plant-derived lipids showed a slower increase in sperm volume over male
 age compared to males reared on yeast-derived lipid food which is richer
 in saturated fatty acids. ii) The resistance of sperm membrane integrity
 to osmotic stress was not altered by dietary lipid treatment but iii) food
 containing yeast-derived lipids induced a 46% higher in-situ rate of
 production of reactive oxygen species in sperm cells. These findings show
 that dietary lipids have similar effects on sperm parameters in Drosophila
 as in vertebrates, affect some, but not all, sperm parameters, and
 modulate male reproductive ageing. In concert with recent findings of
 sex-specific seasonal variation of diet choice in the wild, our results
 suggest a substantial dietary impact on the dynamics of male reproduction
 in the wild.
DOI: 10.5061/dryad.ncjsxksr1
title: Stable species boundaries despite ten million years of hybridization in tropical eels

description: Genomic evidence is increasingly underpinning that hybridization between
 taxa is commonplace, challenging our views on the mechanisms that maintain
 their boundaries. Here, we focus on seven catadromous eel species (genus
 Anguilla), and use genome-wide sequence data from more than 450
 individuals sampled across the tropical Indo-Pacific, morphological
 information, and three newly assembled draft genomes to compare
 contemporary patterns of hybridization with signatures of past gene flow
 across a time-calibrated phylogeny. We show that the seven species have
 remained distinct entities for up to 10 million years, despite a dynamic
 scenario of incomplete isolation whereby the current frequencies of
 hybridization across species pairs (over 5% of all individuals were either
 F1 hybrids or backcrosses) contrast remarkably with patterns of past
 introgression. Based on near-complete asymmetry in the directionality of
 hybridization and decreasing frequencies of later-generation hybrids, we
 identify cytonuclear incompatibilities and hybrid breakdown as two
 powerful mechanisms that can support species cohesion even when
 hybridization has been pervasive throughout the evolutionary history of
 entire clades.
description: A flow chart showing the steps used to generate
 files anguilla_hapl1.fa.gz, anguilla_hapl2.fa.gz, anguilla_aln1.tgz, anguilla_aln2.tgz, anguilla_var1.vcf.gz, anguilla_var2.vcf.gz, and anguilla_var3.vcf.gz is provided as Supplementary Figure 1 of the manuscript. Files angmar.mapped.fq.gz, angmeg.mapped.fq.gz, and angobs.mapped.fq.gz were generated as described in section "Detecting past introgression" of the manuscript. The file dotplots.tgz was generated as described in Supplementary Note 6. Code used to generate and analyze the files of this repository can be found at https://github.com/mmatschiner/anguilla