PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Development of a camera trap for perching dragonflies: a new tool for freshwater environmental assessment
items: Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing
items: Differences in small noncoding RNAs profile between bull X and Y sperm
items: A new tiny toad species of Amazophrynella (Anura: Bufonidae) from east of the Guiana Shield in Amazonia, Brazil
items: Endocranial anatomy of the ceratopsid dinosaur Triceratops and interpretations of sensory and motor function
items: Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony
items: Native trees of Mexico: diversity, distribution, uses and conservation
items: Life-history traits and intra-cohort divergence of clearhead icefish (Protosalanx chinensis), indicating cannibalism increased fitness
items: Different responses of plant N and P resorption to overgrazing in three dominant species in a typical steppe of Inner Mongolia, China
items: Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies

Development of a camera trap for perching dragonflies: a new tool for freshwater environmental assessment
type: item
type: AcademicArticle
description: Although dragonflies are excellent environmental indicators for monitoring terrestrial water ecosystems, automatic monitoring techniques using digital tools are limited. We designed a novel camera trapping system with an original dragonfly detector based on the hypothesis that perching dragonflies can be automatically detected using inexpensive and energy-saving photosensors built in a perch-like structure. A trial version of the camera trap was developed and evaluated in a case study targeting red dragonflies (Sympetrum spp.) in Japan. During an approximately 2-month period, the detector successfully detected Sympetrum dragonflies while using extremely low power consumption (less than 5 mW). Furthermore, a short-term field experiment using time-lapse cameras for validation at three locations indicated that the detection accuracy was sufficient for practical applications. The frequency of false positive detection ranged from 17 to 51 over an approximately 2-day period. The detection sensitivities were 0.67 and 1.0 at two locations, where a time-lapse camera confirmed that Sympetrum dragonflies perched on the trap more than once. However, the correspondence between the detection frequency by the camera trap and the abundance of Sympetrum dragonflies determined by field observations conducted in parallel was low when the dragonfly density was relatively high. Despite the potential for improvements in our camera trap and its application to the quantitative monitoring of dragonflies, the low cost and low power consumption of the detector make it a promising tool.
format: application/pdf
format: text/html
creator: Akira Yoshioka
creator: Akira Shimizu
creator: Hiroyuki Oguma
creator: Nao Kumada
creator: Keita Fukasawa
creator: Shoma Jingu
creator: Taku Kadoya
subject: Biodiversity
subject: Conservation Biology
subject: Entomology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.9681
publisher: PeerJ Inc.
rights: © 2020 Yoshioka et al.
abstract: Although dragonflies are excellent environmental indicators for monitoring terrestrial water ecosystems, automatic monitoring techniques using digital tools are limited. We designed a novel camera trapping system with an original dragonfly detector based on the hypothesis that perching dragonflies can be automatically detected using inexpensive and energy-saving photosensors built in a perch-like structure. A trial version of the camera trap was developed and evaluated in a case study targeting red dragonflies (Sympetrum spp.) in Japan. During an approximately 2-month period, the detector successfully detected Sympetrum dragonflies while using extremely low power consumption (less than 5 mW). Furthermore, a short-term field experiment using time-lapse cameras for validation at three locations indicated that the detection accuracy was sufficient for practical applications. The frequency of false positive detection ranged from 17 to 51 over an approximately 2-day period. The detection sensitivities were 0.67 and 1.0 at two locations, where a time-lapse camera confirmed that Sympetrum dragonflies perched on the trap more than once. However, the correspondence between the detection frequency by the camera trap and the abundance of Sympetrum dragonflies determined by field observations conducted in parallel was low when the dragonfly density was relatively high. Despite the potential for improvements in our camera trap and its application to the quantitative monitoring of dragonflies, the low cost and low power consumption of the detector make it a promising tool.
bibliographic citation: Yoshioka et al. (2020) Development of a camera trap for perching dragonflies: a new tool for freshwater environmental assessment. PeerJ 8:e9681 https://doi.org/10.7717/peerj.9681
date submitted: 2020-03-30
date accepted: 2020-07-17
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yoshioka
  given name: Akira
author list: Agent
  family name: Shimizu
  given name: Akira
author list: Agent
  family name: Oguma
  given name: Hiroyuki
author list: Agent
  family name: Kumada
  given name: Nao
author list: Agent
  family name: Fukasawa
  given name: Keita
author list: Agent
  family name: Jingu
  given name: Shoma
author list: Agent
  family name: Kadoya
  given name: Taku
doi: 10.7717/peerj.9681
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Yoshioka et al.
attribution name: Yoshioka et al.

Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing
type: item
type: AcademicArticle
description: Current projections suggest that climate warming will be accompanied by more frequent and severe drought events. Peatlands store ca. one third of the world’s soil organic carbon. Warming and drought may cause peatlands to become carbon sources through stimulation of microbial activity increasing ecosystem respiration, with positive feedback effect on global warming. Micro-eukaryotes play a key role in the carbon cycle through food web interactions and therefore, alterations in their community structure and diversity may affect ecosystem functioning and could reflect these changes. We assessed the diversity and community composition of Sphagnum-associated eukaryotic microorganisms inhabiting peatlands and their response to experimental drought and warming using high throughput sequencing of environmental DNA. Under drier conditions, micro-eukaryotic diversity decreased, the relative abundance of autotrophs increased and that of osmotrophs (including Fungi and Peronosporomycetes) decreased. Furthermore, we identified climate change indicators that could be used as early indicators of change in peatland microbial communities and ecosystem functioning. The changes we observed indicate a shift towards a more “terrestrial” community in response to drought, in line with observed changes in the functioning of the ecosystem.
format: application/pdf
format: text/html
creator: Monika K. Reczuga
creator: Christophe Victor William Seppey
creator: Matthieu Mulot
creator: Vincent E.J. Jassey
creator: Alexandre Buttler
creator: Sandra Słowińska
creator: Michał Słowiński
creator: Enrique Lara
creator: Mariusz Lamentowicz
creator: Edward A.D. Mitchell
subject: Biodiversity
subject: Ecology
subject: Soil Science
subject: Climate Change Biology
description: doi:10.7717/peerj.9821
publisher: PeerJ Inc.
rights: © 2020 Reczuga et al.
abstract: Current projections suggest that climate warming will be accompanied by more frequent and severe drought events. Peatlands store ca. one third of the world’s soil organic carbon. Warming and drought may cause peatlands to become carbon sources through stimulation of microbial activity increasing ecosystem respiration, with positive feedback effect on global warming. Micro-eukaryotes play a key role in the carbon cycle through food web interactions and therefore, alterations in their community structure and diversity may affect ecosystem functioning and could reflect these changes. We assessed the diversity and community composition of Sphagnum-associated eukaryotic microorganisms inhabiting peatlands and their response to experimental drought and warming using high throughput sequencing of environmental DNA. Under drier conditions, micro-eukaryotic diversity decreased, the relative abundance of autotrophs increased and that of osmotrophs (including Fungi and Peronosporomycetes) decreased. Furthermore, we identified climate change indicators that could be used as early indicators of change in peatland microbial communities and ecosystem functioning. The changes we observed indicate a shift towards a more “terrestrial” community in response to drought, in line with observed changes in the functioning of the ecosystem.
bibliographic citation: Reczuga et al. (2020) Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing. PeerJ 8:e9821 https://doi.org/10.7717/peerj.9821
date submitted: 2019-11-10
date accepted: 2020-08-05
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reczuga
  given name: Monika K.
author list: Agent
  family name: Seppey
  given name: Christophe Victor William
author list: Agent
  family name: Mulot
  given name: Matthieu
author list: Agent
  family name: Jassey
  given name: Vincent E.J.
author list: Agent
  family name: Buttler
  given name: Alexandre
author list: Agent
  family name: Słowińska
  given name: Sandra
author list: Agent
  family name: Słowiński
  given name: Michał
author list: Agent
  family name: Lara
  given name: Enrique
author list: Agent
  family name: Lamentowicz
  given name: Mariusz
author list: Agent
  family name: Mitchell
  given name: Edward A.D.
doi: 10.7717/peerj.9821
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Reczuga et al.
attribution name: Reczuga et al.

Differences in small noncoding RNAs profile between bull X and Y sperm
type: item
type: AcademicArticle
description: The differences in small noncoding RNAs (sncRNAs), including miRNAs, piRNAs, and tRNA-derived fragments (tsRNAs), between X and Y sperm of mammals remain unclear. Here, we employed high-throughput sequencing to systematically compare the sncRNA profiles of X and Y sperm from bulls (n = 3), which may have a wider implication for the whole mammalian class. For the comparison of miRNA profiles, we found that the abundance of bta-miR-652 and bta-miR-378 were significantly higher in X sperm, while nine miRNAs, including bta-miR-204 and bta-miR-3432a, had greater abundance in Y sperm (p < 0.05). qPCR was then used to further validate their abundances. Subsequent functional analysis revealed that their targeted genes in sperm were significantly involved in nucleosome binding and nucleosomal DNA binding. In contrast, their targeted genes in mature oocyte were significantly enriched in 11 catabolic processes, indicating that these differentially abundant miRNAs may trigger a series of catabolic processes for the catabolization of different X and Y sperm components during fertilization. Furthermore, we found that X and Y sperm showed differences in piRNA clusters distributed in the genome as well as piRNA and tsRNA abundance, two tsRNAs (tRNA-Ser-AGA and tRNA-Ser-TGA) had lower abundance in X sperm than Y sperm (p < 0.05). Overall, our work describes the different sncRNA profiles of X and Y sperm in cattle and enhances our understanding of their potential roles in the regulation of sex differences in sperm and early embryonic development.
format: application/pdf
format: text/html
creator: Hao Zhou
creator: Jiajia Liu
creator: Wei Sun
creator: Rui Ding
creator: Xihe Li
creator: Aishao Shangguan
creator: Yang Zhou
creator: Tesfaye Worku
creator: Xingjie Hao
creator: Faheem Ahmed Khan
creator: Liguo Yang
creator: Shujun Zhang
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.9822
publisher: PeerJ Inc.
rights: © 2020 Zhou et al.
abstract: The differences in small noncoding RNAs (sncRNAs), including miRNAs, piRNAs, and tRNA-derived fragments (tsRNAs), between X and Y sperm of mammals remain unclear. Here, we employed high-throughput sequencing to systematically compare the sncRNA profiles of X and Y sperm from bulls (n = 3), which may have a wider implication for the whole mammalian class. For the comparison of miRNA profiles, we found that the abundance of bta-miR-652 and bta-miR-378 were significantly higher in X sperm, while nine miRNAs, including bta-miR-204 and bta-miR-3432a, had greater abundance in Y sperm (p < 0.05). qPCR was then used to further validate their abundances. Subsequent functional analysis revealed that their targeted genes in sperm were significantly involved in nucleosome binding and nucleosomal DNA binding. In contrast, their targeted genes in mature oocyte were significantly enriched in 11 catabolic processes, indicating that these differentially abundant miRNAs may trigger a series of catabolic processes for the catabolization of different X and Y sperm components during fertilization. Furthermore, we found that X and Y sperm showed differences in piRNA clusters distributed in the genome as well as piRNA and tsRNA abundance, two tsRNAs (tRNA-Ser-AGA and tRNA-Ser-TGA) had lower abundance in X sperm than Y sperm (p < 0.05). Overall, our work describes the different sncRNA profiles of X and Y sperm in cattle and enhances our understanding of their potential roles in the regulation of sex differences in sperm and early embryonic development.
bibliographic citation: Zhou et al. (2020) Differences in small noncoding RNAs profile between bull X and Y sperm. PeerJ 8:e9822 https://doi.org/10.7717/peerj.9822
date submitted: 2020-06-24
date accepted: 2020-08-05
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Hao
author list: Agent
  family name: Liu
  given name: Jiajia
author list: Agent
  family name: Sun
  given name: Wei
author list: Agent
  family name: Ding
  given name: Rui
author list: Agent
  family name: Li
  given name: Xihe
author list: Agent
  family name: Shangguan
  given name: Aishao
author list: Agent
  family name: Zhou
  given name: Yang
author list: Agent
  family name: Worku
  given name: Tesfaye
author list: Agent
  family name: Hao
  given name: Xingjie
author list: Agent
  family name: Khan
  given name: Faheem Ahmed
author list: Agent
  family name: Yang
  given name: Liguo
author list: Agent
  family name: Zhang
  given name: Shujun
doi: 10.7717/peerj.9822
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Zhou et al.
attribution name: Zhou et al.

A new tiny toad species of Amazophrynella (Anura: Bufonidae) from east of the Guiana Shield in Amazonia, Brazil
type: item
type: AcademicArticle
description: The combination of different approaches has successfully delimited new species within many Neotropical species complexes traditionally classified as a single nominal organism. Recent studies have shown that the Amazonian endemic genus Amazophrynella, currently composed of 12 small-sized species, could harbor several additional species. Based on morphology and molecular data, we describe a new species of Amazophrynella from east of the Guiana Shield, in Pará state, Brazil. The new species is characterized by having one of the biggest size of the genus (SVL of males 16.0–17.8 mm and females 22.9–24.4 mm), presence of a large palmar tubercle (occupying 2/4 of the palmar surface), 5.6–8.1% uncorrected p-distance from its sister clade (including A. teko, A. sp.1, and A. manaos) for the 16S mitochondrial gene, and 8.8% for the COI. The new species described here represents a newly discovered lineage. Of the 12 Amazophrynella species currently recognized, two were describe in the last century (A. bokermanni and A. minuta) and the remaining species were recently discovered and described (in the last six years), which underscores the degree to which species richness of Amazophrynella is underestimated.
format: application/pdf
format: text/html
creator: Sarah Mângia
creator: Ricardo Koroiva
creator: Diego José Santana
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9887
publisher: PeerJ Inc.
rights: © 2020 Mângia et al.
abstract: The combination of different approaches has successfully delimited new species within many Neotropical species complexes traditionally classified as a single nominal organism. Recent studies have shown that the Amazonian endemic genus Amazophrynella, currently composed of 12 small-sized species, could harbor several additional species. Based on morphology and molecular data, we describe a new species of Amazophrynella from east of the Guiana Shield, in Pará state, Brazil. The new species is characterized by having one of the biggest size of the genus (SVL of males 16.0–17.8 mm and females 22.9–24.4 mm), presence of a large palmar tubercle (occupying 2/4 of the palmar surface), 5.6–8.1% uncorrected p-distance from its sister clade (including A. teko, A. sp.1, and A. manaos) for the 16S mitochondrial gene, and 8.8% for the COI. The new species described here represents a newly discovered lineage. Of the 12 Amazophrynella species currently recognized, two were describe in the last century (A. bokermanni and A. minuta) and the remaining species were recently discovered and described (in the last six years), which underscores the degree to which species richness of Amazophrynella is underestimated.
bibliographic citation: Mângia et al. (2020) A new tiny toad species of Amazophrynella (Anura: Bufonidae) from east of the Guiana Shield in Amazonia, Brazil. PeerJ 8:e9887 https://doi.org/10.7717/peerj.9887
date submitted: 2020-04-07
date accepted: 2020-08-17
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mângia
  given name: Sarah
author list: Agent
  family name: Koroiva
  given name: Ricardo
author list: Agent
  family name: Santana
  given name: Diego José
doi: 10.7717/peerj.9887
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Mângia et al.
attribution name: Mângia et al.

Endocranial anatomy of the ceratopsid dinosaur Triceratops and interpretations of sensory and motor function
type: item
type: AcademicArticle
description: Triceratops is one of the well-known Cretaceous ceratopsian dinosaurs. The ecology of Triceratops has been controversial because of its unique morphological features. However, arguments based on brain and inner ear structures have been scarce. In this study, two braincases (FPDM-V-9677 and FPDM-V-9775) were analyzed with computed tomography to generate three-dimensional virtual renderings of the endocasts of the cranial cavities and bony labyrinths. Quantitative analysis, including comparison of linear measurements of the degree of development of the olfactory bulb and inner ear, was performed on these virtual endocasts to acquire detailed neuroanatomical information. When compared with other dinosaurs, the olfactory bulb of Triceratops is relatively small, indicating that Triceratops had a reduced acuity in sense of smell. The lateral semicircular canal reveals that the basicranial axis of Triceratops is approximately 45° to the ground, which is an effective angle to display their horns as well as frill, and to graze. The semicircular canals of Triceratops are relatively smaller than those of primitive ceratopsians, such as Psittacosaurus and Protoceratops, suggesting that sensory input for the reflexive stabilization of gaze and posture of Triceratops was less developed than that of primitive ceratopsians. The cochlear length of Triceratops is relatively short when compared with other dinosaurs. Because cochlear length correlates with hearing frequency, Triceratops was likely adapted to hearing low frequencies.
format: application/pdf
format: text/html
creator: Rina Sakagami
creator: Soichiro Kawabe
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.9888
publisher: PeerJ Inc.
rights: © 2020 Sakagami and Kawabe
abstract: Triceratops is one of the well-known Cretaceous ceratopsian dinosaurs. The ecology of Triceratops has been controversial because of its unique morphological features. However, arguments based on brain and inner ear structures have been scarce. In this study, two braincases (FPDM-V-9677 and FPDM-V-9775) were analyzed with computed tomography to generate three-dimensional virtual renderings of the endocasts of the cranial cavities and bony labyrinths. Quantitative analysis, including comparison of linear measurements of the degree of development of the olfactory bulb and inner ear, was performed on these virtual endocasts to acquire detailed neuroanatomical information. When compared with other dinosaurs, the olfactory bulb of Triceratops is relatively small, indicating that Triceratops had a reduced acuity in sense of smell. The lateral semicircular canal reveals that the basicranial axis of Triceratops is approximately 45° to the ground, which is an effective angle to display their horns as well as frill, and to graze. The semicircular canals of Triceratops are relatively smaller than those of primitive ceratopsians, such as Psittacosaurus and Protoceratops, suggesting that sensory input for the reflexive stabilization of gaze and posture of Triceratops was less developed than that of primitive ceratopsians. The cochlear length of Triceratops is relatively short when compared with other dinosaurs. Because cochlear length correlates with hearing frequency, Triceratops was likely adapted to hearing low frequencies.
bibliographic citation: Sakagami et al. (2020) Endocranial anatomy of the ceratopsid dinosaur Triceratops and interpretations of sensory and motor function. PeerJ 8:e9888 https://doi.org/10.7717/peerj.9888
date submitted: 2020-03-12
date accepted: 2020-08-17
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sakagami
  given name: Rina
author list: Agent
  family name: Kawabe
  given name: Soichiro
doi: 10.7717/peerj.9888
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Sakagami and Kawabe
attribution name: Sakagami and Kawabe

Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony
type: item
type: AcademicArticle
description: The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including DQA, DRA, DQB, and DRB, and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. DRA had the lowest dN/dS ratio (0.560) compared with the other three loci, indicating that DRA was conserved and could be conserved after undergoing selective processes. Nine DQA, five DQB, nine DRA, and seven DRB codons were under significant positive selection at the antigen binding sites (ABS), suggesting that the selected residues in ABS may play a significant role in the innate immune system of the GZP. Two GZP alleles were shared with Przewalski’s horse, and six older GZP haplotypes had a better relationship with other horse species by one or two mutational steps, indicating that the GZP may be a natural ancient variety of equid. The specific diversity of ABS and the numbers of unique haplotypes in the evolutionary process affords this species a better genetic fitness and ability to adapt to the native environment.
format: application/pdf
format: text/html
creator: Chang Liu
creator: Hongmei Lei
creator: Xueqin Ran
creator: Jiafu Wang
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.9889
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including DQA, DRA, DQB, and DRB, and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. DRA had the lowest dN/dS ratio (0.560) compared with the other three loci, indicating that DRA was conserved and could be conserved after undergoing selective processes. Nine DQA, five DQB, nine DRA, and seven DRB codons were under significant positive selection at the antigen binding sites (ABS), suggesting that the selected residues in ABS may play a significant role in the innate immune system of the GZP. Two GZP alleles were shared with Przewalski’s horse, and six older GZP haplotypes had a better relationship with other horse species by one or two mutational steps, indicating that the GZP may be a natural ancient variety of equid. The specific diversity of ABS and the numbers of unique haplotypes in the evolutionary process affords this species a better genetic fitness and ability to adapt to the native environment.
bibliographic citation: Liu et al. (2020) Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony. PeerJ 8:e9889 https://doi.org/10.7717/peerj.9889
date submitted: 2019-11-25
date accepted: 2020-08-17
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Chang
author list: Agent
  family name: Lei
  given name: Hongmei
author list: Agent
  family name: Ran
  given name: Xueqin
author list: Agent
  family name: Wang
  given name: Jiafu
doi: 10.7717/peerj.9889
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Liu et al.
attribution name: Liu et al.

Native trees of Mexico: diversity, distribution, uses and conservation
type: item
type: AcademicArticle
description: Background Mexico is one of the most floristically rich countries in the world. Despite significant contributions made on the understanding of its unique flora, the knowledge on its diversity, geographic distribution and human uses, is still largely fragmented. Unfortunately, deforestation is heavily impacting this country and native tree species are under threat. The loss of trees has a direct impact on vital ecosystem services, affecting the natural capital of Mexico and people’s livelihoods. Given the importance of trees in Mexico for many aspects of human well-being, it is critical to have a more complete understanding of their diversity, distribution, traditional uses and conservation status. We aimed to produce the most comprehensive database and catalogue on native trees of Mexico by filling those gaps, to support their in situ and ex situ conservation, promote their sustainable use, and inform reforestation and livelihoods programmes. Methods A database with all the tree species reported for Mexico was prepared by compiling information from herbaria and reviewing the available floras. Species names were reconciled and various specialised sources were used to extract additional species information, i.e. endemic status, threat status, availability in seed collections, reports on plant uses and conservation actions currently in place. With this information, a comprehensive catalogue of native trees from Mexico was redacted. Available georeferenced records were used to map each species distribution and perform spatial analyses to identify gaps of information and priority areas for their conservation and exploration. Results Mexico has at least 2,885 native tree species, belonging to 612 genera and 128 families. Fabaceae is the most represented family and Quercus the most represented genus. Approximately 44% of tree species are endemic to the country. The southern part of the country showed the highest values of species richness. Six hundred and seventy-four spec…
format: application/pdf
format: text/html
creator: Oswaldo Tellez
creator: Efisio Mattana
creator: Mauricio Diazgranados
creator: Nicola Kühn
creator: Elena Castillo-Lorenzo
creator: Rafael Lira
creator: Leobardo Montes-Leyva
creator: Isela Rodriguez
creator: Cesar Mateo Flores Ortiz
creator: Michael Way
creator: Patricia Dávila
creator: Tiziana Ulian
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Plant Science
description: doi:10.7717/peerj.9898
publisher: PeerJ Inc.
rights: © 2020 Tellez et al.
abstract: Background Mexico is one of the most floristically rich countries in the world. Despite significant contributions made on the understanding of its unique flora, the knowledge on its diversity, geographic distribution and human uses, is still largely fragmented. Unfortunately, deforestation is heavily impacting this country and native tree species are under threat. The loss of trees has a direct impact on vital ecosystem services, affecting the natural capital of Mexico and people’s livelihoods. Given the importance of trees in Mexico for many aspects of human well-being, it is critical to have a more complete understanding of their diversity, distribution, traditional uses and conservation status. We aimed to produce the most comprehensive database and catalogue on native trees of Mexico by filling those gaps, to support their in situ and ex situ conservation, promote their sustainable use, and inform reforestation and livelihoods programmes. Methods A database with all the tree species reported for Mexico was prepared by compiling information from herbaria and reviewing the available floras. Species names were reconciled and various specialised sources were used to extract additional species information, i.e. endemic status, threat status, availability in seed collections, reports on plant uses and conservation actions currently in place. With this information, a comprehensive catalogue of native trees from Mexico was redacted. Available georeferenced records were used to map each species distribution and perform spatial analyses to identify gaps of information and priority areas for their conservation and exploration. Results Mexico has at least 2,885 native tree species, belonging to 612 genera and 128 families. Fabaceae is the most represented family and Quercus the most represented genus. Approximately 44% of tree species are endemic to the country. The southern part of the country showed the highest values of species richness. Six hundred and seventy-four spec…
bibliographic citation: Tellez et al. (2020) Native trees of Mexico: diversity, distribution, uses and conservation. PeerJ 8:e9898 https://doi.org/10.7717/peerj.9898
date submitted: 2020-05-04
date accepted: 2020-08-17
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tellez
  given name: Oswaldo
author list: Agent
  family name: Mattana
  given name: Efisio
author list: Agent
  family name: Diazgranados
  given name: Mauricio
author list: Agent
  family name: Kühn
  given name: Nicola
author list: Agent
  family name: Castillo-Lorenzo
  given name: Elena
author list: Agent
  family name: Lira
  given name: Rafael
author list: Agent
  family name: Montes-Leyva
  given name: Leobardo
author list: Agent
  family name: Rodriguez
  given name: Isela
author list: Agent
  family name: Flores Ortiz
  given name: Cesar Mateo
author list: Agent
  family name: Way
  given name: Michael
author list: Agent
  family name: Dávila
  given name: Patricia
author list: Agent
  family name: Ulian
  given name: Tiziana
doi: 10.7717/peerj.9898
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Tellez et al.
attribution name: Tellez et al.

Life-history traits and intra-cohort divergence of clearhead icefish (Protosalanx chinensis), indicating cannibalism increased fitness
type: item
type: AcademicArticle
description: Cannibalism is considered one of the causes of intra-cohort size divergence in fish and is usually believed to result in increased fitness in terms of survival and reproduction, but direct evidence of this is lacking. Population demographics of the clearhead icefish (Protosalanx chinensis) from Lake Xingkai (Khanka) were investigated for one year. Size-frequencies exhibited a bimodal distribution from July through January, where the population diverged into an upper and a lower modal group based on size. Stomach content analysis confirmed the occurrence of cannibalism, where fish belonging to the larger, upper modal group preyed upon those of the smaller, lower modal group. We found P. chinensis does not spawn until all of the oocytes have reached maturity and then a single spawning event occurs although the oocytes may develope asynchronously in the ovary. Upper modal group females matured slightly earlier than those of the lower modal group, and reproductive investment was considerably greater in the upper modal group than the lower modal group. The lower modal males made up the majority of the population after the spawning period, which meant they may have few opportunities to participate in reproduction. Therefore, piscivory and cannibalism of P. chinensis appears to have increased fitness of the fish belonging to the upper modal group and greatly reduced the fitness of those belonging to the lower modal group.
format: application/pdf
format: text/html
creator: Fujiang Tang
creator: Wei Liu
creator: Jilong Wang
creator: James Henne
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.9900
publisher: PeerJ Inc.
rights: © 2020 Tang et al.
abstract: Cannibalism is considered one of the causes of intra-cohort size divergence in fish and is usually believed to result in increased fitness in terms of survival and reproduction, but direct evidence of this is lacking. Population demographics of the clearhead icefish (Protosalanx chinensis) from Lake Xingkai (Khanka) were investigated for one year. Size-frequencies exhibited a bimodal distribution from July through January, where the population diverged into an upper and a lower modal group based on size. Stomach content analysis confirmed the occurrence of cannibalism, where fish belonging to the larger, upper modal group preyed upon those of the smaller, lower modal group. We found P. chinensis does not spawn until all of the oocytes have reached maturity and then a single spawning event occurs although the oocytes may develope asynchronously in the ovary. Upper modal group females matured slightly earlier than those of the lower modal group, and reproductive investment was considerably greater in the upper modal group than the lower modal group. The lower modal males made up the majority of the population after the spawning period, which meant they may have few opportunities to participate in reproduction. Therefore, piscivory and cannibalism of P. chinensis appears to have increased fitness of the fish belonging to the upper modal group and greatly reduced the fitness of those belonging to the lower modal group.
bibliographic citation: Tang et al. (2020) Life-history traits and intra-cohort divergence of clearhead icefish (Protosalanx chinensis), indicating cannibalism increased fitness. PeerJ 8:e9900 https://doi.org/10.7717/peerj.9900
date submitted: 2020-02-27
date accepted: 2020-08-18
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Tang
  given name: Fujiang
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Wang
  given name: Jilong
author list: Agent
  family name: Henne
  given name: James
doi: 10.7717/peerj.9900
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Tang et al.
attribution name: Tang et al.

Different responses of plant N and P resorption to overgrazing in three dominant species in a typical steppe of Inner Mongolia, China
type: item
type: AcademicArticle
description: Nutrient resorption from senesced leaves is an important mechanism for nutrient conservation in plants. However, little is known about the effect of grazing on plant nutrient resorption from senesced leaves, especially in semiarid ecosystems. Here, we evaluated the effects of grazing on N and P resorption in the three most dominant grass species in a typical steppe in northern China. We identified the key pathways of grazing-induced effects on N and P resorption efficiency. Grazing increased N and P concentrations in the green leaves of Leymus chinensis and Stipa grandis but not in Cleistogenes squarossa. Both L. chinensis and S. grandis exhibited an increasing trend of leaf N resorption, whereas C. squarrosa recorded a decline in both leaf N and P resorption efficiency under grazing. Structural equation models showed that grazing is the primary driver of the changes in N resorption efficiency of the three dominant grass species. For L. chinensis, the P concentration in green and senesced leaves increased the P resorption efficiency, whereas the senesced leaf P concentration played an important role in the P resorption efficiency of C. squarrosa. Grazing directly drove the change in P resorption efficiency of S. grandis. Our results suggest that large variations in nutrient resorption patterns among plant species depend on leaf nutritional status and nutrient-use strategies under overgrazing, and indicate that overgrazing may have indirect effects on plant-mediated nutrient cycling via inducing shifts in the dominance of the three plant species.
format: application/pdf
format: text/html
creator: Zhen Wang
creator: Saheed Olaide Jimoh
creator: Xiliang Li
creator: Baoming Ji
creator: Paul C. Struik
creator: Shixian Sun
creator: Ji Lei
creator: Yong Ding
creator: Yong Zhang
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
description: doi:10.7717/peerj.9915
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Nutrient resorption from senesced leaves is an important mechanism for nutrient conservation in plants. However, little is known about the effect of grazing on plant nutrient resorption from senesced leaves, especially in semiarid ecosystems. Here, we evaluated the effects of grazing on N and P resorption in the three most dominant grass species in a typical steppe in northern China. We identified the key pathways of grazing-induced effects on N and P resorption efficiency. Grazing increased N and P concentrations in the green leaves of Leymus chinensis and Stipa grandis but not in Cleistogenes squarossa. Both L. chinensis and S. grandis exhibited an increasing trend of leaf N resorption, whereas C. squarrosa recorded a decline in both leaf N and P resorption efficiency under grazing. Structural equation models showed that grazing is the primary driver of the changes in N resorption efficiency of the three dominant grass species. For L. chinensis, the P concentration in green and senesced leaves increased the P resorption efficiency, whereas the senesced leaf P concentration played an important role in the P resorption efficiency of C. squarrosa. Grazing directly drove the change in P resorption efficiency of S. grandis. Our results suggest that large variations in nutrient resorption patterns among plant species depend on leaf nutritional status and nutrient-use strategies under overgrazing, and indicate that overgrazing may have indirect effects on plant-mediated nutrient cycling via inducing shifts in the dominance of the three plant species.
bibliographic citation: Wang et al. (2020) Different responses of plant N and P resorption to overgrazing in three dominant species in a typical steppe of Inner Mongolia, China. PeerJ 8:e9915 https://doi.org/10.7717/peerj.9915
date submitted: 2020-05-26
date accepted: 2020-08-19
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhen
author list: Agent
  family name: Jimoh
  given name: Saheed Olaide
author list: Agent
  family name: Li
  given name: Xiliang
author list: Agent
  family name: Ji
  given name: Baoming
author list: Agent
  family name: Struik
  given name: Paul C.
author list: Agent
  family name: Sun
  given name: Shixian
author list: Agent
  family name: Lei
  given name: Ji
author list: Agent
  family name: Ding
  given name: Yong
author list: Agent
  family name: Zhang
  given name: Yong
doi: 10.7717/peerj.9915
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies
type: item
type: AcademicArticle
description: Dietary habits in extinct species cannot be directly observed; thus, in the absence of extraordinary evidence, they must be reconstructed with a combination of morphological proxies. Such proxies often include information on dental organization and function such as tooth formation time and tooth replacement rate. In extinct organisms, tooth formation times and tooth replacement rate are calculated, in part via extrapolation of the space between incremental lines in dental tissues representing daily growth (von Ebner Line Increment Width; VEIW). However, to date, little work has been conducted testing assumptions about the primary data underpinning these calculations, specifically, the potential impact of differential sampling and data extrapolation protocols. To address this, we tested a variety of intradental, intramandibular, and ontogentic sampling effects on calculations of mean VEIW, tooth formation times, and replacement rates using histological sections and CT reconstructions of a growth series of three specimens of the extant archosaurian Alligator mississippiensis. We find transect position within the tooth and transect orientation with respect to von Ebner lines to have the greatest impact on calculations of mean VEIW—a maximum number of VEIW measurements should be made as near to the central axis (CA) as possible. Measuring in regions away from the central axis can reduce mean VEIW by up to 36%, causing inflated calculations of tooth formation time. We find little demonstrable impact to calculations of mean VEIW from the practice of subsampling along a transect, or from using mean VEIW derived from one portion of the dentition to extrapolate for other regions of the dentition. Subsampling along transects contributes only minor variations in mean VEIW (<12%) that are dwarfed by the standard deviation (SD). Moreover, variation in VEIW with distance from the pulp cavity likely reflects idiosyncratic patterns related to life history, which are difficult to co…
format: application/pdf
format: text/html
creator: Jens C.D. Kosch
creator: Lindsay E. Zanno
subject: Paleontology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.9918
publisher: PeerJ Inc.
rights: © 2020 Kosch and Zanno
abstract: Dietary habits in extinct species cannot be directly observed; thus, in the absence of extraordinary evidence, they must be reconstructed with a combination of morphological proxies. Such proxies often include information on dental organization and function such as tooth formation time and tooth replacement rate. In extinct organisms, tooth formation times and tooth replacement rate are calculated, in part via extrapolation of the space between incremental lines in dental tissues representing daily growth (von Ebner Line Increment Width; VEIW). However, to date, little work has been conducted testing assumptions about the primary data underpinning these calculations, specifically, the potential impact of differential sampling and data extrapolation protocols. To address this, we tested a variety of intradental, intramandibular, and ontogentic sampling effects on calculations of mean VEIW, tooth formation times, and replacement rates using histological sections and CT reconstructions of a growth series of three specimens of the extant archosaurian Alligator mississippiensis. We find transect position within the tooth and transect orientation with respect to von Ebner lines to have the greatest impact on calculations of mean VEIW—a maximum number of VEIW measurements should be made as near to the central axis (CA) as possible. Measuring in regions away from the central axis can reduce mean VEIW by up to 36%, causing inflated calculations of tooth formation time. We find little demonstrable impact to calculations of mean VEIW from the practice of subsampling along a transect, or from using mean VEIW derived from one portion of the dentition to extrapolate for other regions of the dentition. Subsampling along transects contributes only minor variations in mean VEIW (<12%) that are dwarfed by the standard deviation (SD). Moreover, variation in VEIW with distance from the pulp cavity likely reflects idiosyncratic patterns related to life history, which are difficult to co…
bibliographic citation: Kosch et al. (2020) Sampling impacts the assessment of tooth growth and replacement rates in archosaurs: implications for paleontological studies. PeerJ 8:e9918 https://doi.org/10.7717/peerj.9918
date submitted: 2020-04-03
date accepted: 2020-08-20
issued: 2020-09-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kosch
  given name: Jens C.D.
author list: Agent
  family name: Zanno
  given name: Lindsay E.
doi: 10.7717/peerj.9918
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-18
copyright: © 2020 Kosch and Zanno
attribution name: Kosch and Zanno

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359