Apéndice A

Lista completa de MPP en orquídeas

En esta sección se hace una recopilación de los estudios de dinámica poblacional en orquídeas que han usado matrices de transición de estados y de edades. Se identifican algunos de los temas principales de los trabajos.

En la siguiente tabla se presentan los estudios de dinámica poblacional en orquídeas que usaron MPP y las preguntas principales que los autores intentaron responder. En la gran mayoría de los trabajos se evalúan múltiples hipótesis/ideas sobre la dinámica poblacional de las orquídeas. Para información específica sobre la metodología usada en cada estudio, se recomienda revisar los trabajos originales.

Clave de las variables:
- Riesgo: Si se evaluó el riesgo de extinción de la especie.
- Variación espacial: Si se evaluó la variación espacial de la especie.
- Variación temporal: Si se evaluó la variación temporal de la especie.
- Latencia: Si se evaluó la importancia de la latencia (dormancy) de la especie.
- Métodos de estimación de parámetros: Si se evaluaron métodos alternos de estimación de parámetros (no tradicionales).
- Historia de vida: Si se evaluó la historia de vida de la especie en un contexto evolutivo.
- Otro: Si se evaluó otra pregunta no incluida en las anteriores.
- Referencia: Referencia del estudio.

Código

library(readr)
library(tidyverse)
library(dplyr)
library(gt)
library(flextable) # fallback para Word/PDF cuando gt::as_word falla
library(ftExtra)   # colformat_md() para procesar *italics* en celdas

Código

listsp <- dplyr::tribble(
  ~"Genero", ~Especies, ~Riesgo, ~"Var esp.", ~"Var temp", ~"Lat", ~"Est param", ~"Hist vida", ~Otro, ~Ref,
  "*Aspasia*", "*principissa*", "Si", "-", "Si", "-", "-", "-", "-", "@zotz2006population",
  "*Brassavola*", "*cucullata*", "Si", "Si", "Si", "-", "-", "-", "IPM, Transient Dynamics, Transfer Function", "@ackerman2020small",
  "*Broughtonia*", "*cubensis*", "Si", "Si", "Si", "-", "-", "-", "Transient Dynamics", "@raventos2021effects",
  "*Caladenia*", "*amoena*", "Si", "-", "-", "Si", "Si", "Si", "Selección de modelos, método para estimar latencia", "@tremblay2009population @tremblay2009dormancy; ",
  "*Caladenia*", "*argocalla*", "Si", "-", "-", "Si", "Si", "Si", "Selección de modelos, método para estimar latencia", "@tremblay2009population @tremblay2009dormancy",
  "*Caladenia*", "*clavigera*", "Si", "-", "-", "Si", "Si", "Si", "Selección de modelos, método para estimar latencia", "@tremblay2009population  @tremblay2009dormancy",
  "*Caladenia*", "*elegans*", "Si", "-", "-", "Si", "Si", "Si", "Selección de modelos, método para estimar latencia", "@tremblay2009population @tremblay2009dormancy",
  "*Caladenia*", "*graniticola*", "Si", "-", "-", "Si", "Si", "Si", "Selección de modelos, método para estimar latencia", "@tremblay2009population @tremblay2009dormancy",
  "*Caladenia*", "*macroclavia*", "Si", "-", "-", "Si", "Si", "Si", "Selección de modelos, método para estimar latencia", "@tremblay2009population @tremblay2009dormancy",
  "*Caladenia*", "*oenochila*", "Si", "-", "-", "Si", "Si", "Si", "Selección de modelos, método para estimar latencia", "@tremblay2009population @tremblay2009dormancy",
  "*Caladenia*", "*rosella*", "Si", "-", "-", "Si", "Si", "Si", "Selección de modelos, método para estimar latencia", "@tremblay2009population @tremblay2009dormancy",
  "*Caladenia*", "*valida*", "Si", "-", "-", "Si", "Si", "Si", "Selección de modelos, método para estimar latencia", "@tremblay2009population @tremblay2009dormancy",
  "*Caladenia*", "*orientalis*", "Si", "Si", "Si", "Si", "-", "-", "Interacciones abióticas", "@coates2009demographic",
  "*Cephalanthera*", "*longifolia*", "-", "-", "-", "Si", "Si", "Si", "Interacciones abióticas y bióticas", "@shefferson2012linking",
  "*Cleistes*", "*divaricata* var. *divaricata*", "Si", "Si", "Si", "Si", "Si", "-", "-", "@gregg1991variation",
  "*Cleistes*", "*divaricata* var. *bifaria*", "Si", "Si", "Si", "Si", "Si", "-", "-", "@gregg1991variation",
  "*Cleistes*", "*bifaria*", "-", "Si", "-", "Si", "-", "-", "Estructura de tamaño y estado", "@gregg2006comparison",
  "*Corallorhiza*", "*trifida*", "Si", "-", "Si", "Si", "-", "-", "-", "@iriondo2009peligro",
  "*Crepidium*", "*acuminatum*", "Si", "-", "Si", "-", "-", "-", "Efecto de cosecha", "@timsina2021six",
  "*Cypripedium*", "*acaule*", "-", "-", "-", "-", "Si", "-", "Edad de individuos reproductivos", "@cochran1992simple",
  "*Cypripedium*", "*calceolus*", "Si", "Si", "Si", "Si", "-", "-", "Selección de modelos", "@nicole2005population",
  "*Cypripedium*", "*calceolus*", "Si", "Si", "Si", "Si", "-", "-", "Efecto de aislamiento", "@garcia2010living",
  "*Cypripedium*", "*calceolus*", "-", "-", "-", "-", "-", "-", "Costo de latencia, Interacciones abióticas y bióticas", "@shefferson2012linking",
  "*Cypripedium*", "*fasciculatum*", "Si", "Si", "Si", "Si", "-", "-", "Selección de modelos, Interacciones abióticas", "@thorpe2011trends",
  "*Cypripedium*", "*parviflorum*", "-", "-", "-", "Si", "-", "Si", "-", "@shefferson2014life",
  "*Cypripedium*", "*reginae*", "-", "Si", "-", "Si", "-", "Si", "Selección de modelos, interacciones bióticas", "@kery2004demographic",
  "*Cypripedium*", "*lentiginosum*", "-", "-", "-", "-", "Si", "-", "Leslie matrix", "@zhongjian2008correlation",
  "*Dactylorhiza*", "*hatagirea*", "Si", "Si", "Si", "Si", "-", "-", "Efecto de cosecha", "@chapagain2021illegal",
  "*Dactylorhiza*", "*lapponica*", "-", "Si", "Si", "Si", "-", "-", "Efecto antropogénico, interacciones abióticas", "@sletvold2010long; @sletvold2013climate",
  "*Dendrophylax*", "*lindenii*", "Si", "-", "Si", "-", "-", "-", "Efecto de densidad, **los datos de la matriz no están disponibles**", "@gonzalez2009dinamica; @raventos2015population",
  "*Epidendrum*", "*xanthinum*", "Si", "Si", "-", "-", "-", "-", "Comparación de poblaciones", "@farfan2008estrategias",
  "*Epipactis*", "*atrorubens*", "Si", "Si", "Si", "Si ", "-", "-", "Incorporación de variable de endogamia", "@hens2017low",
  "*Epipactis*", "*atrorubens*", "-", "-", "-", "- ", "-", "-", "", "@jakalaniemi2011orchids",
  "*Erycina*", "*crista-galli*", "Si", "Si", "-", "-", "-", "-", "-", "@mondragon2007life",
  "*Erycina*", "*crista-galli*", "-", "-", "-", "-", "-", "-", "-", "@maldonado2005patron",
  "*Guarianthe*", "*aurantiaca*", "Si", "Si", "-", "-", "-", "-", "Efecto de cosecha", "@mondragon2009population",
  "*Herminium*", "*monorchis*", "Si", "-", "Si", "Si", "-", "-", "Efecto abiótico", "@wells1998flowering",
  "*Himantoglossum*", "*hircinum*", "Si", "-", "Si", "-", "-", "-", "Efecto abiótico: sequía", "@wells1998flowering",
  "*Himantoglossum*", "*hircinum*", "Si", "-", "Si", "-", "-", "-", "Modelando expansión", "@carey1998modelling",
  "*Himantoglossum*", "*hircinum*", "Si", "-", "Si", "Si", "-", "-", "Efecto abiótico: Precipitación y Temp del suelo", "@pfeifer2006influence",
  "*Isotria*", "*medeoloides*", "Si", "-", "Si", "-", "-", "-", "Tratamiento del dosel", "@dibble2019demography",
  "*Jacquiniella*", "*leucomelana*", "Si", "-", "Si", "-", "-", "-", "Metapopulation approach", "@winkler2009population",
  "*Jacquiniella*", "*teretifolia*", "Si", "-", "Si", "-", "-", "-", "Metapopulation approach", "@winkler2009population",
  "*Laelia*", "*autumnalis*", "Si", "Si", "Si", "-", "-", "", "Efecto de cosecha", "@emeterio2021does",
  "*Laelia*", "*speciosa*", "Si", "-", "Si", "-", "-", "-", "Efecto de cosecha", "@hernandez1992dinamica",
  "*Lepanthes*", "*caritensis*", "Si", "Si", "Si", "-", "-", "-", "-", "@tremblay1997lepanthes",
  "*Lepanthes*", "*caritensis*", "Si", "Si", "Si", "-", "-", "-", "Efecto de huracanes", "@crain2019sheltered",
  "*Lepanthes*", "*eltoroensis*", "Si", "Si", "-", "-", "-", "-", "Tamaño efectivo de Población, Ne y largo de vida", "@tremblay2001gene",
  "*Lepanthes*", "*eltoroensis*", "Si", "Si", "Si", "-", "-", "-", "-", "@tremblay2003population",
  "*Lepanthes*", "*eltoroensis*", "Si", "Si", "Si", "Si", "-", "-", "Nueva metodología para estimar parámetros", "@tremblay2021population",
  "*Lepanthes*", "*rubripetala*", "-", "-", "-", "-", "-", "-", "Tamaño efectivo de Población, Ne y largo de vida", "@tremblay2001gene",
  "*Lepanthes*", "*rubripetala*", "Si", "Si", "Si", "-", "-", "-", "Dinámica de transiciones", "@tremblay2015stable",
  "*Lepanthes*", "*rupestris*", "-", "-", "-", "-", "-", "-", "Tamaño efectivo de Población, Ne y largo de vida", "@tremblay2001gene",
  "*Lepanthes*", "*acuminata*", "Si", "-", "-", "-", "-", "-", "Dinámica de transiciones", "@raventos2018comparison",
  "*Lycaste*", "*aromatica*", "Si", "-", "Si", "-", "-", "-", "Metapopulation approach", "@winkler2009population",
  "*Neotinea*", "*ustulata*", "Si", "Si", "-", "Si", "-", "Si", "Método para estimar latencia", "@shefferson2007dormancy",
  "*Oeceoclades*", "*maculata*", "Si", "Si", "Si", "-", "-", "-", "Especie invasiva", "@riveron2019spatio",
  "*Oncidium*", "*poikilostalix*", "Si", "-", "-", "-", "-", "-", "Dinámica de transiciones", "@raventos2018comparison",
  "*Orchis*", "*purpurea*", "Si", "-", "Si", "-", "-", "-", "LTRE", "@jacquemyn2010seed",
  "*Orchis*", "*ustulata*", "Si", "Si", "-", "-", "-", "-", "mismo que *Neotinea ustulata*", "@tali2002dynamics",
  "*Phaius*", "*australis*", "Si", "Si", "-", "-", "-", "-", "Efecto espacial y abiótico", "@simmons2016Viability",
  "*Platanthera*", "*hookeri*", "Si", "Si", "-", "-", "-", "-", "-", "@reddoch2007population",
  "*Platanthera*", "*praeclara*", "Si", "Si", "Si", "Si", "-", "-", "Variación temporal", "@sieg1995influence",
  "*Platanthera*", "*macrophylla*", "Si", "Si", "Si", "-", "-", "-", "Incluye estado de protocormo", "@cleavitt2017life @berry2021population",
  "*Platanthera*", "*orbiculata*", "Si", "Si", "Si", "-", "-", "-", "Incluye estado de protocormo", "@cleavitt2017life @berry2021population",
  "*Prasophyllum*", "*correctum*", "Si", "", "Si", "Si", "-", "-", "Efecto de fuego", "@coates2006effects",
  "*Pseudorchis*", "*albida*", "-", "-", "-", "-", "-", "-", "-", "@stipkova2013mowing",
  "*Rodriguezia*", "*granadensis*", "Si", "Si", "Si", "-", "-", "", "Efecto antropogénico, **to be digitized**", "@ospina2023effect",
  "*Serapias*", "*cordigera*", "Si", "Si", "Si", "Si", "-", "-", "Efecto antropogénico", "@pellegrino2014effects",
  "*Spathoglottis*", "*plicata*", "Si", "Si", "Si", "-", "-", "-", "Orquídea invasiva y interacciones bióticas", "@falcon2017quantifying",
  "*Spiranthes*", "*delitescens*", "Si", "Si", "Si", "Si", "-", "-", "Efecto abiótico: sequía", "@mcclaran1992population",
  "*Spiranthes*", "*parksii*", "Si", "", "-", "-", "-", "-", "Efecto abiótico: herbivoría", "@wonka2010herbivores",
  "*Telipogon*", "*helleri*", "Si", "-", "-", "-", "-", "Si", "Dinámica de transición", "@raventos2018comparison",
  "*Tolumnia*", "*variegata*", "Si", "Si", "Si", "-", "-", "Si", "El costo de reproducción", "@calvo1993evolutionary",
  "*Trichocentrum*", "*undulatum*", "-", "-", "-", "-", "-", "", "Efecto de aislamiento", "@borrero2023populations"
)

Código

# gt::as_word() es buggy con contenido markdown (incluye @-citations);
# falla con `subscript out of bounds` en docx. Usamos gt para HTML
# (donde renderiza bien) y flextable + ftExtra::colformat_md para Word/PDF.
if (knitr::is_html_output()) {
  listsp |>
    gt() |>
    fmt_markdown(columns = c(Genero, Especies, Otro, Ref)) |>
    cols_label(
      Genero      = "Género",
      Especies    = "Especies",
      Riesgo      = "Riesgo",
      `Var esp.`  = "Var. esp.",
      `Var temp`  = "Var. temp.",
      Lat         = "Latencia",
      `Est param` = "Est. param.",
      `Hist vida` = "Hist. vida",
      Otro        = "Otro",
      Ref         = "Referencia"
    ) |>
    cols_align(align = "left", columns = everything()) |>
    tab_options(
      table.font.names          = c("Libertinus Serif", "Iowan Old Style", "Palatino", "Georgia"),
      table.font.size           = px(12),
      column_labels.font.size   = px(12),
      column_labels.font.weight = "bold",
      table.width               = pct(100),
      data_row.padding          = px(4)
    )
} else {
  listsp |>
    as.data.frame() |>
    flextable() |>
    flextable::set_header_labels(
      `Var esp.` = "Var. esp.", `Var temp` = "Var. temp.",
      Lat = "Latencia", `Est param` = "Est. param.",
      `Hist vida` = "Hist. vida", Genero = "Género", Ref = "Referencia"
    ) |>
    ftExtra::colformat_md(j = c("Genero", "Especies", "Otro", "Ref")) |>
    ft_wide()
}

Género	Especies	Riesgo	Var. esp.	Var. temp.	Latencia	Est. param.	Hist. vida	Otro	Referencia
Aspasia	principissa	Si	-	Si	-	-	-		Zotz y Schmidt (2006)
Brassavola	cucullata	Si	Si	Si	-	-	-	IPM, Transient Dynamics, Transfer Function	Ackerman et al. (2020)
Broughtonia	cubensis	Si	Si	Si	-	-	-	Transient Dynamics	Raventós et al. (2021)
Caladenia	amoena	Si	-	-	Si	Si	Si	Selección de modelos, método para estimar latencia	Tremblay et al. (2009a) Tremblay et al. (2009b);
Caladenia	argocalla	Si	-	-	Si	Si	Si	Selección de modelos, método para estimar latencia	Tremblay et al. (2009a) Tremblay et al. (2009b)
Caladenia	clavigera	Si	-	-	Si	Si	Si	Selección de modelos, método para estimar latencia	Tremblay et al. (2009a) Tremblay et al. (2009b)
Caladenia	elegans	Si	-	-	Si	Si	Si	Selección de modelos, método para estimar latencia	Tremblay et al. (2009a) Tremblay et al. (2009b)
Caladenia	graniticola	Si	-	-	Si	Si	Si	Selección de modelos, método para estimar latencia	Tremblay et al. (2009a) Tremblay et al. (2009b)
Caladenia	macroclavia	Si	-	-	Si	Si	Si	Selección de modelos, método para estimar latencia	Tremblay et al. (2009a) Tremblay et al. (2009b)
Caladenia	oenochila	Si	-	-	Si	Si	Si	Selección de modelos, método para estimar latencia	Tremblay et al. (2009a) Tremblay et al. (2009b)
Caladenia	rosella	Si	-	-	Si	Si	Si	Selección de modelos, método para estimar latencia	Tremblay et al. (2009a) Tremblay et al. (2009b)
Caladenia	valida	Si	-	-	Si	Si	Si	Selección de modelos, método para estimar latencia	Tremblay et al. (2009a) Tremblay et al. (2009b)
Caladenia	orientalis	Si	Si	Si	Si	-	-	Interacciones abióticas	Coates y Duncan (2009)
Cephalanthera	longifolia	-	-	-	Si	Si	Si	Interacciones abióticas y bióticas	Shefferson et al. (2012)
Cleistes	divaricata var. divaricata	Si	Si	Si	Si	Si	-		Gregg (1991)
Cleistes	divaricata var. bifaria	Si	Si	Si	Si	Si	-		Gregg (1991)
Cleistes	bifaria	-	Si	-	Si	-	-	Estructura de tamaño y estado	Gregg y Kéry (2006)
Corallorhiza	trifida	Si	-	Si	Si	-	-		Iriondo Alegria et al. (2009)
Crepidium	acuminatum	Si	-	Si	-	-	-	Efecto de cosecha	Timsina et al. (2021)
Cypripedium	acaule	-	-	-	-	Si	-	Edad de individuos reproductivos	Cochran y Ellner (1992)
Cypripedium	calceolus	Si	Si	Si	Si	-	-	Selección de modelos	Nicolè et al. (2005)
Cypripedium	calceolus	Si	Si	Si	Si	-	-	Efecto de aislamiento	Garcı́a et al. (2010)
Cypripedium	calceolus	-	-	-	-	-	-	Costo de latencia, Interacciones abióticas y bióticas	Shefferson et al. (2012)
Cypripedium	fasciculatum	Si	Si	Si	Si	-	-	Selección de modelos, Interacciones abióticas	Thorpe et al. (2011)
Cypripedium	parviflorum	-	-	-	Si	-	Si		Shefferson et al. (2014)
Cypripedium	reginae	-	Si	-	Si	-	Si	Selección de modelos, interacciones bióticas	Kéry y Gregg (2004)
Cypripedium	lentiginosum	-	-	-	-	Si	-	Leslie matrix	Zhongjian et al. (2008)
Dactylorhiza	hatagirea	Si	Si	Si	Si	-	-	Efecto de cosecha	Chapagain et al. (2021)
Dactylorhiza	lapponica	-	Si	Si	Si	-	-	Efecto antropogénico, interacciones abióticas	Sletvold et al. (2010); Sletvold et al. (2013)
Dendrophylax	lindenii	Si	-	Si	-	-	-	Efecto de densidad, los datos de la matriz no están disponibles	González-Hernández (2009); Raventós et al. (2015)
Epidendrum	xanthinum	Si	Si	-	-	-	-	Comparación de poblaciones	Farfán Camargo (2008)
Epipactis	atrorubens	Si	Si	Si	Si	-	-	Incorporación de variable de endogamia	Hens et al. (2017)
Epipactis	atrorubens	-	-	-	-	-	-		Jäkäläniemi et al. (2011)
Erycina	crista-galli	Si	Si	-	-	-	-		Mondragón et al. (2007)
Erycina	crista-galli	-	-	-	-	-	-		Maldonado Flores (2005)
Guarianthe	aurantiaca	Si	Si	-	-	-	-	Efecto de cosecha	Mondragón (2009)
Herminium	monorchis	Si	-	Si	Si	-	-	Efecto abiótico	Wells et al. (1998)
Himantoglossum	hircinum	Si	-	Si	-	-	-	Efecto abiótico: sequía	Wells et al. (1998)
Himantoglossum	hircinum	Si	-	Si	-	-	-	Modelando expansión	Carey (1998)
Himantoglossum	hircinum	Si	-	Si	Si	-	-	Efecto abiótico: Precipitación y Temp del suelo	Pfeifer y Jetschke (2006)
Isotria	medeoloides	Si	-	Si	-	-	-	Tratamiento del dosel	Dibble et al. (2019)
Jacquiniella	leucomelana	Si	-	Si	-	-	-	Metapopulation approach	Winkler et al. (2009)
Jacquiniella	teretifolia	Si	-	Si	-	-	-	Metapopulation approach	Winkler et al. (2009)
Laelia	autumnalis	Si	Si	Si	-	-		Efecto de cosecha	Emeterio-Lara et al. (2021)
Laelia	speciosa	Si	-	Si	-	-	-	Efecto de cosecha	Hernández-Apolinar (1992)
Lepanthes	caritensis	Si	Si	Si	-	-	-		Tremblay (1997)
Lepanthes	caritensis	Si	Si	Si	-	-	-	Efecto de huracanes	Crain et al. (2019)
Lepanthes	eltoroensis	Si	Si	-	-	-	-	Tamaño efectivo de Población, Ne y largo de vida	Tremblay y Ackerman (2001)
Lepanthes	eltoroensis	Si	Si	Si	-	-	-		Tremblay y Hutchings (2003)
Lepanthes	eltoroensis	Si	Si	Si	Si	-	-	Nueva metodología para estimar parámetros	Tremblay et al. (2021)
Lepanthes	rubripetala	-	-	-	-	-	-	Tamaño efectivo de Población, Ne y largo de vida	Tremblay y Ackerman (2001)
Lepanthes	rubripetala	Si	Si	Si	-	-	-	Dinámica de transiciones	Tremblay et al. (2015)
Lepanthes	rupestris	-	-	-	-	-	-	Tamaño efectivo de Población, Ne y largo de vida	Tremblay y Ackerman (2001)
Lepanthes	acuminata	Si	-	-	-	-	-	Dinámica de transiciones	Raventós et al. (2018)
Lycaste	aromatica	Si	-	Si	-	-	-	Metapopulation approach	Winkler et al. (2009)
Neotinea	ustulata	Si	Si	-	Si	-	Si	Método para estimar latencia	Shefferson y Tali (2007)
Oeceoclades	maculata	Si	Si	Si	-	-	-	Especie invasiva	Riverón-Giró et al. (2019)
Oncidium	poikilostalix	Si	-	-	-	-	-	Dinámica de transiciones	Raventós et al. (2018)
Orchis	purpurea	Si	-	Si	-	-	-	LTRE	Jacquemyn et al. (2010)
Orchis	ustulata	Si	Si	-	-	-	-	mismo que Neotinea ustulata	Tali (2002)
Phaius	australis	Si	Si	-	-	-	-	Efecto espacial y abiótico	Simmons (2016)
Platanthera	hookeri	Si	Si	-	-	-	-		Reddoch y Reddoch (2007)
Platanthera	praeclara	Si	Si	Si	Si	-	-	Variación temporal	Sieg y King (1995)
Platanthera	macrophylla	Si	Si	Si	-	-	-	Incluye estado de protocormo	Cleavitt et al. (2017) Berry y Cleavitt (2021)
Platanthera	orbiculata	Si	Si	Si	-	-	-	Incluye estado de protocormo	Cleavitt et al. (2017) Berry y Cleavitt (2021)
Prasophyllum	correctum	Si		Si	Si	-	-	Efecto de fuego	Coates et al. (2006)
Pseudorchis	albida	-	-	-	-	-	-		Štípková (2013)
Rodriguezia	granadensis	Si	Si	Si	-	-		Efecto antropogénico, to be digitized	Ospina-Calderón et al. (2023)
Serapias	cordigera	Si	Si	Si	Si	-	-	Efecto antropogénico	Pellegrino y Bellusci (2014)
Spathoglottis	plicata	Si	Si	Si	-	-	-	Orquídea invasiva y interacciones bióticas	Falcón et al. (2017)
Spiranthes	delitescens	Si	Si	Si	Si	-	-	Efecto abiótico: sequía	McClaran y Sundt (1992)
Spiranthes	parksii	Si		-	-	-	-	Efecto abiótico: herbivoría	Wonka (2010)
Telipogon	helleri	Si	-	-	-	-	Si	Dinámica de transición	Raventós et al. (2018)
Tolumnia	variegata	Si	Si	Si	-	-	Si	El costo de reproducción	Calvo (1993)
Trichocentrum	undulatum	-	-	-	-	-		Efecto de aislamiento	Borrero et al. (2023)

Figura 1: *Trichocentrum undulatum*. Foto: Hong Liu

Código

#### https://cran.r-project.org/web/packages/ftExtra/vignettes/format_columns.html # Enlace para formatear columnas que tiene referencias en formato markdown

Notas para añadir a la tabla

IPM - Integrated Population Model
Transient dynamics
Transfer function

Especies de orquídeas estudiadas sin MPP

En la siguiente lista incluimos algunos de los trabajos de dinámica poblacional que no usan MPP para responder a su pregunta. La lista es muy grande y no es exhaustiva. Incluye trabajos que usan otros métodos de estimación de parámetros, como modelos de regresión, o que usan IPM (Integral Population Models), pero no usan matrices de transición de estados o edades, que es el método alterno de estimación de parámetros que se usa en este libro.

Figura 2: *Spiranthes delitescens*. Foto: Mitchel McClaran

Código

NO_matrix <- dplyr::tribble(
  ~"Genero", ~Especies, ~Otro, ~Ref,
  "*Isotria*", "*medeoloides*", "no matrix", "@alahuhta2017instant",
  "*Cyclopogon*", "*luteoalbus*", "no matrix", "@juarez2014viability",
  "*Cypripedium*", "*calceolus*", "no matrix", "@davison2013contributions",
  "*Cypripedium*", "*candidum*", "no matrix", "@shefferson2017predicting",
  "*Gymnadenia*", "*conopsea*", "no matrix", "@oien2002flowering",
  "*Ophrys*", "*sphegodes*", "no matrix", "@hutchings2010population",
  "*Ophrys*", "*sphegodes*", "no matrix", "@shefferson2017predicting",
  "*Orchis*", "*morio*", "no matrix", "@wells1998flowering",
  "*Spiranthes*", "*spiralis*", "no matrix", "@jacquemyn2007long"
)

Código

# Mismo patrón que `lista2-gt`: gt para HTML, flextable para Word/PDF
# (gt::as_word es buggy con contenido markdown).
if (knitr::is_html_output()) {
  NO_matrix |>
    gt() |>
    fmt_markdown(columns = c(Genero, Especies, Otro, Ref)) |>
    cols_label(
      Genero   = "Género",
      Especies = "Especies",
      Otro     = "Otro",
      Ref      = "Referencia"
    ) |>
    cols_align(align = "left", columns = everything()) |>
    tab_options(
      table.font.names          = c("Libertinus Serif", "Iowan Old Style", "Palatino", "Georgia"),
      table.font.size           = px(12),
      column_labels.font.size   = px(12),
      column_labels.font.weight = "bold",
      table.width               = pct(100),
      data_row.padding          = px(4)
    )
} else {
  NO_matrix |>
    as.data.frame() |>
    flextable() |>
    flextable::set_header_labels(Genero = "Género", Ref = "Referencia") |>
    ftExtra::colformat_md(j = c("Genero", "Especies", "Otro", "Ref")) |>
    ft_wide()
}

Género	Especies	Otro	Referencia
Isotria	medeoloides	no matrix	Alahuhta et al. (2017)
Cyclopogon	luteoalbus	no matrix	Juárez et al. (2014)
Cypripedium	calceolus	no matrix	Davison et al. (2013)
Cypripedium	candidum	no matrix	Shefferson et al. (2017)
Gymnadenia	conopsea	no matrix	Øien y Moen (2002)
Ophrys	sphegodes	no matrix	Hutchings (2010)
Ophrys	sphegodes	no matrix	Shefferson et al. (2017)
Orchis	morio	no matrix	Wells et al. (1998)
Spiranthes	spiralis	no matrix	Jacquemyn et al. (2007)

Ackerman, J., Tremblay, R., Pérez, M., Madden, H., Bechtold, M., & Boeken, M. (2020). Small populations on small islands: What chance does an orchid have? International Journal of Plant Sciences, 181, 667-685.

Alahuhta, K., Crone, E., Ettinger, A., Hens, H., Jäkäläniemi, A., & Tuomi, J. (2017). Instant death, slow death and the consequences of assumptions about prolonged dormancy for plant population dynamics. Journal of Ecology, 105, 471-483.

Berry, E. J., & Cleavitt, N. L. (2021). Population dynamics and comparative demographics in sympatric populations of the round-leaved orchids Platanthera macrophylla and P. orbiculata. Population Ecology, 63, 274-289.

Borrero, H., Oviedo-Prieto, R., Alvarez, J. C., Ticktin, T., Cisneros, M., & Liu, H. (2023). Populations of a tropical epiphytic orchid are destabilized in its peripheral range by hurricane and an exotic herbivore. Ecosphere, 14, e4355.

Calvo, R. N. (1993). Evolutionary demography of orchids: intensity and frequency of pollination and the cost of fruiting. Ecology, 74, 1033-1042. https://doi.org/10.2307/1940473

Carey, P. (1998). Modelling the spread of Himantoglossum hircinum (L.) Spreng. at a site in the south of England. Botanical Journal of the Linnean Society, 126, 159-172.

Chapagain, D. J., Meilby, H., Baniya, C. B., Budha-Magar, S., & Ghimire, S. K. (2021). Illegal harvesting and livestock grazing threaten the endangered orchid Dactylorhiza hatagirea (D. Don) Soó in Nepalese Himalaya. Ecology and evolution, 11, 6672-6687.

Cleavitt, N. L., Berry, E. J., Hautaniemi, J., & Fahey, T. J. (2017). Life stages, demographic rates, and leaf damage for the round-leaved orchids, Platanthera orbiculata (Pursh.) Lindley and P. macrophylla (Goldie) PM Brown in a northern hardwood forest in New Hampshire, USA. Botany, 95, 61-71.

Coates, F., & Duncan, M. (2009). Demographic variation between populations of Caladenia orientalis–a fire-managed threatened orchid. Australian Journal of Botany, 57, 326-339.

Coates, F., Lunt, I. D., & Tremblay, R. (2006). Effects of disturbance on population dynamics of the threatened orchid Prasophyllum correctum DL Jones and implications for grassland management in south-eastern Australia. Biological Conservation, 129, 59-69.

Cochran, M. E., & Ellner, S. (1992). Simple Methods for Calculating Age-Based Life History Parameters for Stage-Structured Populations: Ecological Archives M062-002. Ecological monographs, 62, 345-364.

Crain, B., Tremblay, R., & Ferguson, J. (2019). Sheltered from the storm? Population viability analysis of a rare endemic under periodic catastrophe regimes. Population Ecology, 61, 74-92. https://doi.org/10.1002/1438-390X.1002

Davison, R., Nicole, F., Jacquemyn, H., & Tuljapurkar, S. (2013). Contributions of covariance: decomposing the components of stochastic population growth in Cypripedium calceolus. The American Naturalist, 181, 410-420.

Dibble, A. C., Gawler, S. C., Wright, W. A., Vitt, P., Cameron, D. S., Bajcz, A. W., & Campbell, C. S. (2019). Demography of the rare orchid, Isotria medeoloides (Orchidaceae) and its response to a canopy thinning treatment. Rhodora, 121, 67-107.

Emeterio-Lara, A., Garcı́a-Franco, J. G., Hernández-Apolinar, M., Toledo-Hernández, V. H., Valencia-Dı́az, S., & Flores-Palacios, A. (2021). Does extraction of orchids affect their population structure? Evidence from populations of Laelia autumnalis (Orchidaceae). Forest Ecology and Management, 480, 118667.

Falcón, W., Ackerman, J. D., & Tremblay, R. (2017). Quantifying how acquired interactions with native and invasive insects influence population growth rates of a non-indigenous plant. Biological Invasions, 19, 895-911. https://doi.org/10.1007/s10530-016-1318-8

Farfán Camargo, J. (2008). Estrategias reproductivas de la orquídea Epidendrum xanthinum Lindl., en la Cordillera Occidental, Valle del Cauca. mathesis. Bogotá, Colombia: Universidad Nacional de Colombia.

Garcı́a, M. B., Goni, D., & Guzmán, D. (2010). Living at the edge: Local versus positional factors in the long-term population dynamics of an endangered orchid. Conservation biology, 24, 1219-1229.

González-Hernández, E. (2009). Dinámica de las poblaciones estructuradas en clases de vida de dos especies de la familia Orchidaceae: Broughtonia cubensis (Lindley) Cogniaux y Dendrophylax lindenii (Lindley) Bentham et Rolfe, en el Cabo San Antonio, Península de Guanahacabibes, Cuba. Modelos matriciales de proyección lineal. Tesis doctoral. Centro de Investigaciones y Servicios Ambientales ECOVIDA Pinar del Río, Cuba: Universidad de ALicante, Spain.

Gregg, K. B. (1991). Variation in Behaviour of four populations of the orchid Cleistes divaricata, an assessment using transition matriz models. In: Wells, T. C. E., & Willems, J. H. (eds.), Population Ecology of Terrestrial Orchids (pp. 139-159). SPB Academic Publishing bv, The Hague.

Gregg, K. B., & Kéry, M. (2006). Comparison of size vs. life-state classification in demographic models for the terrestrial orchid Cleistes bifaria. Biological Conservation, 129, 50-58.

Hens, H., Pakanen, V.-M., Jäkäläniemi, A., Tuomi, J., & Kvist, L. (2017). Low population viability in small endangered orchid populations: Genetic variation, seedling recruitment and stochasticity. Biological Conservation, 210, 174-183.

Hernández-Apolinar, M. (1992). Dinámica poblacional de Laelia speciosa (HBK) Schltr. (Orchidaceae). mathesis. Mexico City, Mexico.

Hutchings, M. (2010). The population biology of the early spider orchid Ophrys sphegodes Mill. III. Demography over three decades. Journal of Ecology, 98, 867-878.

Iriondo Alegria, J., Albert Gamboa, M., Gimenez Benavides, L., Dominguez Lozano, F., & Escudero Alcantara, A. (2009). Poblaciones en Peligro: Viabilidad Demográfica de la flora vascular amenazada de Espana. Direccion General de Medio Ambiente y Politica Forestal.

Jacquemyn, H., Brys, R., Hermy, M., & Willems, J. H. (2007). Long-term dynamics and population viability in one of the last populations of the endangered Spiranthes spiralis (Orchidaceae) in the Netherlands. Biological Conservation, 134, 14-21.

Jacquemyn, H., Brys, R., & Jongejans, E. (2010). Seed limitation restricts population growth in shaded populations of a perennial woodland orchid. Ecology, 91, 119-129.

Jäkäläniemi, A., Crone, E. E., Närhi, P., & Tuomi, J. (2011). Orchids do not pay costs at emergence for prolonged dormancy. Ecology, 92, 1538-1543.

Juárez, L., Montaña, C., & Franco, M. (2014). The viability of two populations of the terrestrial orchid Cyclopogon luteoalbus in a fragmented tropical mountain cloud forest: Dormancy delays extinction. Biological conservation, 170, 162-168.

Kéry, M., & Gregg, K. B. (2004). Demographic analysis of dormancy and survival in the terrestrial orchid Cypripedium reginae. Journal of Ecology, 92, 686-695.

Maldonado Flores, C. (2005). Patrón de crecimiento y reproducción de la orquı́dea Epidendrum xanthinum Lindl. en la Cordillera Occidental, Valle del Cauca. mathesis. Instituto Politecnico Nacional, Santa Cruz Xoxocotlán, Oaxaca.

McClaran, M. P., & Sundt, P. C. (1992). Population dynamics of the rare orchid, Spiranthes delitescens. The Southwestern Naturalist, 37, 299-303.

Mondragón, D. (2009). Population viability analysis for Guarianthe aurantiaca, an ornamental epiphytic orchid harvested in Southeast México. Plant species biology, 24, 35-41.

Mondragón, D., Maldonado, C., & Aguilar-Santelises, R. (2007). Life history and demography of a twig epiphyte: a case study of Erycina crista-galli (Orchidaceae). Selbyana, 137-144.

Nicolè, F., Brzosko, E., & Till-Bottraud, I. (2005). Population viability analysis of Cypripedium calceolus in a protected area: longevity, stability and persistence. Journal of Ecology, 93, 716-726.

Øien, D.-I., & Moen, A. (2002). Flowering and survival of Dactylorhiza lapponica and Gymnadenia conopsea in the Sølendet Nature Reserve, Central Norway. In: Kindlmann, P., JH, W., & Whigham, D. (eds.), Trends and Fluctuations and Underlying Mechanisms in Terrestrial Orchid Populations (pp. 3-22). Backhuys Publishers, Leiden, The Netherlands.

Ospina-Calderón, N., Tremblay, R., Torres, A., & Flanagan, N. (2023). The effect of habitat transformation on a twig epiphytic orchid: Evidence from population dynamics. Frontiers in Ecology and Evolution, 11, 1135316.

Pellegrino, G., & Bellusci, F. (2014). Effects of human disturbance on reproductive success and population viability of Serapias cordigera (Orchidaceae). Botanical Journal of the Linnean Society, 176, 408-420.

Pfeifer, M., & Jetschke, G. (2006). Influence of geographical isolation on genetic diversity of Himantoglossum hircinum (Orchidaceae). Folia Geobotanica, 41, 3-20.

Raventós, J., Garcı́a-González, A., Riverón-Giró, F. B., & Damon, A. (2018). Comparison of transient and asymptotic perturbation analyses of three epiphytic orchid species growing in coffee plantations in Mexico: effect on conservation decisions. Plant Ecology & Diversity, 11, 133-145.

Raventós, J., González, E., Mújica, E., & Doak, D. F. (2015). Population Viability Analysis of the Epiphytic Ghost Orchid (Dendrophylax lindenii) in Cuba. Biotropica, 47, 179-189.

Raventós, J., Mújica, E., Gonzalez, E., Bonet, A., & Ortega-Larrocea, M. P. (2021). The effects of hurricanes on the stochastic population growth of the endemic epiphytic orchid Broughtonia cubensis living in Cuba. Population Ecology, 63, 302-312.

Reddoch, J. M., & Reddoch, A. H. (2007). Population ecology of Platanthera hookeri (Orchidaceae) in southwestern Quebec, Canada. The Journal of the Torrey Botanical Society, 134, 369-378.

Riverón-Giró, F. B., Raventós, J., Damon, A., Garcı́a-González, A., & Mújica, E. (2019). Spatio-temporal dynamics of the invasive orchid Oeceoclades maculata (Orchidaceae), in four different habitats in southeast Chiapas, Mexico. Biological Invasions, 21, 1905-1919.

Shefferson, R. P., Kull, T., Tali, K., & Kellett, K. M. (2012). Linking vegetative dormancy to fitness in two long-lived herbaceous perennials. Ecosphere, 3, 1-19. https://doi.org/10.1890/ES11-00328.1

Shefferson, R. P., Mizuta, R., & Hutchings, M. J. (2017). Predicting evolution in response to climate change: the example of sprouting probability in three dormancy-prone orchid species. Royal Society Open Science, 4, 160647.

Shefferson, R. P., & Tali, K. (2007). Dormancy is associated with decreased adult survival in the burnt orchid, Neotinea ustulata. Journal of Ecology, 95, 217-225.

Shefferson, R. P., Warren, R. J., & Pulliam, H. R. (2014). Life-history costs make perfect sprouting maladaptive in two herbaceous perennials. Journal of Ecology, 102, 1318-1328.

Sieg, C. H., & King, R. M. (1995). Influence of environmental factors and preliminary demographic analyses of a threatened orchid, Platanthera praeclara. American Midland Naturalist, 307-323.

Simmons, C. (2016). Conservation genetics and population viability of the endangered swamp orchid Phaius australis (Orchidaceae) in a changing world. Tesis doctoral. Faculty of Science, Health, Education; Engineering, University of the Sunshine Coast, Queensland, Australia: University of the Sunshine Coast.

Sletvold, N., Dahlgren, J. P., Øien, D.-I., Moen, A., & Ehrlén, J. (2013). Climate warming alters effects of management on population viability of threatened species: results from a 30-year experimental study on a rare orchid. Global Change Biology, 19, 2729-2738.

Sletvold, N., Øien, D.-I., & Moen, A. (2010). Long-term influence of mowing on population dynamics in the rare orchid Dactylorhiza lapponica: the importance of recruitment and seed production. Biological Conservation, 143, 747-755.

Štípková, Z. (2013). Vliv kosení na populační dynamiku silně ohroženého druhu Pseudorchis albida (Orchidaceae).; Effect of mowing on population dynamics of a highly endangered species Pseudorchis albida (Orchidaceae). mathesis. Faculty of Science, University of South Bohemia, Czech Republic.

Tali, K. (2002). Dynamics or Orchis ustulata populations in Estonia. In: Kindlmann, P., JH, W., & Whigham, D. (eds.), Trends and Fluctuations and Underlying Mechanisms in Terrestrial Orchid Populations (pp. 33-42). Backhuys Publishers, Leiden, The Netherlands.

Thorpe, A., Stanley, A., Kaye, T., & P, L. (2011). Population trends, demography, and the effects of environment and disturbance on Cypripedium fasciculatum in southern Oregon. Institute for Applied Ecology, Corvallis, Oregon; USDI Bureau of Land Management, Medford District, Medford, Oregon.

Timsina, B., Kindlmann, P., Münzbergová, Z., & Rokaya, M. B. (2021). Six-year demographic study of the terrestrial orchid, Crepidium acuminatum: implications for conservation. Frontiers in Ecology and Evolution, 9, 676993.

Tremblay, R. (1997). Lepanthes caritensis, an endangered orchid: no sex, no future? Selbyana, 160-166.

Tremblay, R. L., & Hutchings, M. J. (2003). Population dynamics in orchid conservation: a review of analytical methods based on the rare species Lepanthes eltoroensis. In: Orchid Conservation (pp. 183-204). Kota Kinabalu: Natural History Publications (Borneo).

Tremblay, R., & Ackerman, J. (2001). Gene flow and effective population size in Lepanthes (Orchidaceae): a case for genetic drift. Biological Journal of the Linnean Society, 72, 47-62. https://doi.org/10.1006/bijl.2000.0485

Tremblay, R., Raventos, J., & Ackerman, J. (2015). When stable-stage equilibrium is unlikely: integrating transient population dynamics improves asymptotic methods. Annals of Botany, 116, 381-390. https://doi.org/10.1093/aob/mcv031

Tremblay, R., Tyre, A. J., Pérez, M.-E., & Ackerman, J. D. (2021). Population projections from holey matrices: Using prior information to estimate rare transition events. Ecological Modelling, 447, 109526.

Tremblay, Pérez, M., Larcombe, M., Brown, A., Quarmby, J., Bickerton, D., French, G., & Bould, A. (2009b). Dormancy in Caladenia: A Bayesian approach to evaluating latency. Australian Journal of Botany, 57, 340-350.

Tremblay, Pérez, M., Larcombe, M., Brown, A., Quarmby, J., Bickerton, D., French, G., & Bould, A. (2009a). Population dynamics of Caladenia: Bayesian estimates of transition and extinction probabilities. Australian Journal of Botany, 57, 351-360.

Wells, T., Rothery, P., Cox, R., & Bamford, S. (1998). Flowering dynamics of Orchis morio L. and Herminium monorchis (L.) R. Br. at two sites in eastern England. Botanical Journal of the Linnean Society, 126, 39-48.

Winkler, M., Hülber, K., & Hietz, P. (2009). Population dynamics of epiphytic orchids in a metapopulation context. Annals of Botany, 104, 995-1004. https://doi.org/10.1093/aob/mcp188

Wonka, C. (2010). Large herbivores impact on demographic characteristics and population dynamics of an endangered orchid Spiranthes parksii Correll. mathesis. Texas A & M University.

Zhongjian, L., Lijun, C., Wenhui, R., Liqiang, L., & Yuting, Z. (2008). Correlation between numerical dynamics and reproductive behavior in Cypripedium lentiginosum. Acta Ecologica Sinica, 28, 111-121.

Zotz, G., & Schmidt, G. (2006). Population decline in the epiphytic orchid Aspasia principissa. Biological Conservation, 129, 82-90. https://doi.org/10.1016/j.biocon.2005.07.022